Persecution of Hindus refers to the religious persecution inflicted upon Hindus. Hindus have been historically persecuted during Islamic rule of the Indian subcontinent and during the Goa Inquisition. In modern times, Hindus in the Muslim-majority regions of Kashmir, Pakistan and Bangladesh have also suffered persecution.
1. During Islamic rule of the Indian sub-continent
The Muslim conquest of the Indian subcontinent led to widespread carnage because Muslims regarded the Hindus as infidels and therefore slaughtered and converted millions of Hindus. Will Durant argued in his 1935 book "The Story of Civilization: Our Oriental Heritage" (page 459):
“ The Mohammedan conquest of India is probably the bloodiest story in history. The Islamic historians and scholars have recorded with great glee and pride the slaughters of Hindus, forced conversions, abduction of Hindu women and children to slave markets and the destruction of temples carried out by the warriors of Islam during 800 AD to 1700 AD. Millions of Hindus were converted to Islam by sword during this period. ”
There is no official estimate of the total death toll of Hindus at the hands of Muslims.
As Braudel put it: "The levies it had to pay were so crushing that one catastrophic harvest was" enough to unleash famines and epidemics capable of killing a million people at a time. Appalling poverty was the constant counterpart of the conquerors' opulence.
The backward castes of Hinduism suffered worst. Monarchs (belonging to backward castes) such as Khusrau Bhangi Khan, Hemchandra and Garha-Katanga were knocked off their throne and executed. Backward caste saints like Namadeva  were arrested, while women like Kanhopatra were forced to commit suicide. Ghisadis have an “Urdu” title. 
Prof. K.S. Lal, suggests a calculation in his book Growth of Muslim Population in Medieval IndiaMuslim Caste System in India as established by Ziauddin al-Barani in the Fatawa-i Jahandari.  where they were regarded as "Ajlaf" caste and subjected to severe discrimination by the "Ashraf" castes.  which estimates that between the years 1000 AD and 1500 AD the population of Hindus decreased by 80 million. Even those Hindus who converted to Islam were not immune from persecution, which was illustrated by the
1. 1. By Arabs
Muslim conquest of the Indian subcontinent began during the early 8th century, when the UmayyadDamascus, Hajjaj responded to a casus belli provided by the kidnapping of Muslim women and treasures by pirates off the coast of Debal,  by mobilizing an expedition of 6,000 cavalry under Muhammad bin-Qasim in 712 CE. Records from the campaign recorded in the Chach NamaSindhi forces and the enslavement of their dependents. This action was particularly extensive in Debal, of which Qasim is reported to have been under orders to make an example of while freeing both the captured women and the prisoners of a previous failed expedition. Bin Qasim then enlisted the support of the local Jat, Meds and Bhutto tribes and began the process of subduing and conquering the countryside. The capture of towns was also usually accomplished by means of a treaty with a party from among his "enemy", who were then extended special privileges and material rewards.  However, his superior Hajjaj reportedly objected to his method by saying that it would make him look weak and advocated a more hardline military strategy:  governor of record temple demolitions, and mass executions of resisting
“ It appears from your letter that all the rules made by you for the comfort and convenience of your men are strictly in accordance with religious law. But the way of granting pardon prescribed by the law is different from the one adopted by you, for you go on giving pardon to everybody, high or low, without any discretion between a friend and a foe. The great God says in the Koran [47.4]: "0 True believers, when you encounter the unbelievers, strike off their heads." The above command of the Great God is a great command and must be respected and followed. You should not be so fond of showing mercy, as to nullify the virtue of the act. Henceforth grant pardon to no one of the enemy and spare none of them, or else all will consider you a weak-minded man. ”
In a subsequent communication, Hajjaj reiterated that all able-bodied men were to be killed, and that their underage sons and daughters were to be imprisoned and retained as hostages. Qasim obeyed, and on his arrival at the town of Brahminabad massacred between 6,000 and 16,000 of the defending forces.  The historian, Upendra Thakur records the persecution of Hindus and Buddhists:
“ When Muhammad Kasim invaded Sind in 711 AD, Buddhism had no resistance to offer to their fire and steel. The rosary could not be a match for the sword and the terms Love and Peace had no meaning to them. They carried fire and sword wherever they went and obliterated all that came their way. Muhammad triumphantly marched into the country, conquering Debal, Sehwan, Nerun, Brahmanadabad, Alor and Multan one after the other in quick succession, and in less than a year and a half, the far-flung Hindu kingdom was crushed, the great civilization fell back and Sind entered the darkest period of its history. There was a fearful outbreak of religious bigotry in several places and temples were wantonly desecrated. At Debal, the Nairun and Aror temples were demolished and converted into mosques.[Resistors] were put to death and women made captives. The Jizya was exacted with special care.[Hindus] were required to feed Muslim travellers for three days and three nights.  ”
Other historians and archaeologists such as J E Lohuizen-de Leeuw, take the following stance regarding events preceding the sack of Debal:
“ In fact, we have clear evidence that the Arabs were very tolerant towards both Buddhists and Hindus during the rest of the campaign and throughout the time they ruled Sind...Of course that does not mean that no monuments were ever destroyed, for war always means a certain amount of damage to buildings but it does prove that there was no wanton and systematic destruction of each and every religious center of the Buddhists and Hindus in Sind.  ”
1. 2. Mahmud of Ghazni
Mahmud of Ghazni was an Afghan Sultan who invaded the Indian subcontinent during the early 11th century. His campaigns across the gangetic plains are often cited for their iconoclastic plundering and destruction of temples such as those at Mathura and he looked upon their destruction as an act of "jihad". 
Pradyumna Prasad Karan further describes Mahmud's invasion as one in which he put "thousands of Hindus to the sword" and made a pastime of "raising pyramids of the skulls of the Hindus".   Holt et al. hold an opposing view, that he was "no mere robber or bloody thirsty tyrant" . Mahmud shed no blood "except in the exegencies of war",  and was tolerant in dealings with his own Hindu subjects, some of whom rose to high posts in his administration, such as his Hindu General Tilak 
Mahmud of Ghazni sacked the second Somnath Temple in 1026, and looted it of gems and precious stones and the famous Shiva lingam of the temple was destroyed .  Later the temple was demolished by Mughal Emperor Aurangzeb in 1706. 
1. 3. Muhammad Ghori
Muhammad Ghori committed genocide against Hindus at Kol (modern Aligarh), Kalinjar and Varanasi, according to Hasan Nizami's Taj-ul-Maasir, 20,000 Hindu prisoners were slaughtered and their heads offered to crows. 
1. 4. Timur the Lame's Campaign against India
Main article: Timur
Tīmūr bin Taraghay Barlas (Chagatai Turkic: تیمور - Tēmōr, "iron") (1336 - February 1405), known in the West as Tamerlane, was a 14th century warlord of Turco-Mongol descent,    Timurid Empire and Timurid dynasty (1370-1405) in Central Asia, which survived in some form until 1857. Perhaps, he is more commonly known by his pejorative Persian name Timur-e Lang (Persian: تیمور لنگ) which translates to Timur the Lame, as he was lame after sustaining an injury to the leg in battle. conqueror of much of western and central Asia, and founder of the
Informed about civil war in India, Timur began a trek starting in 1397 to invade the territory of the reigning Sultan Nasir-u Din Mehmud of the Tughlaq Dynasty in the north Indian city of Delhi.
Timur crossed the Indus River at Attock on September 24. The capture of towns and villages was often followed by the massacre of their inhabitants and the raping of their women, as well as pillaging to support his massive army. Timur wrote many times in his memoirs of his specific disdain for the 'idolatrous' Hindus, although he also waged war against Muslim Indians during his campaign.
Timur's invasion did not go unopposed and he did meet some resistance during his march to Delhi, most notably by the Sarv Khap coalition in northern India, and the Governor of Meerut. Although impressed and momentarily stalled by the valour of Ilyaas Awan, Timur was able to continue his relentless approach to Delhi, arriving in 1398 to combat the armies of Sultan Mehmud, already weakened by an internal battle for ascension within the royal family.
The Sultan's army was easily defeated on December 17, 1398. Timur entered Delhi and the city was sacked, destroyed, and left in ruins. Before the battle for Delhi, Timur executed more than 100,000 captives.
Timur himself recorded the invasions in his memoirs, collectively known as Tuzk-i-Timuri.  In them, he vividly described the massacre at Delhi:
In a short space of time all the people in the [Delhi] fort were put to the sword, and in the course of one hour the heads of 10,000 infidels were cut off. The sword of Islam was washed in the blood of the infidels, and all the goods and effects, the treasure and the grain which for many a long year had been stored in the fort became the spoil of my soldiers. They set fire to the houses and reduced them to ashes, and they razed the buildings and the fort to the ground....All these infidel Hindus were slain, their women and children, and their property and goods became the spoil of the victors. I proclaimed throughout the camp that every man who had infidel prisoners should put them to death, and whoever neglected to do so should himself be executed and his property given to the informer. When this order became known to the ghazis of Islam, they drew their swords and put their prisoners to death.
One hundred thousand infidels, impious idolators, were on that day slain. Maulana Nasiruddin Umar, a counselor and man of learning, who, in all his life, had never killed a sparrow, now, in execution of my order, slew with his sword fifteen idolatrous Hindus, who were his captives....on the great day of battle these 100,000 prisoners could not be left with the baggage, and that it would be entirely opposed to the rules of war to set these idolaters and enemies of Islam at liberty...no other course remained but that of making them all food for the sword. 
According to Malfuzat-i-Timuri,  Timur targeted Hindus. In his own words, "Excepting the quarter of the saiyids, the 'ulama and the other Musalmans [sic], the whole city was sacked". In his descriptions of the Loni massacre he wrote, "..Next day I gave orders that the Musalman prisoners should be separated and saved."
During the ransacking of Delhi, almost all inhabitants not killed were captured and enslaved.
Timur left Delhi in approximately January 1399. In April he had returned to his own capital beyond the Oxus (Amu Darya). Immense quantities of spoils were taken from India. According to Ruy Gonzáles de Clavijo, 90 captured elephants were employed merely to carry precious stones looted from his conquest, so as to erect a mosque at Samarkand — what historians today believe is the enormous Bibi-Khanym Mosque. Ironically, the mosque was constructed too quickly and suffered greatly from disrepair within a few decades of its construction.
1. 4. 1. Qutb-ud-din Aibak
Historical records compiled by Muslim historian Maulana Hakim Saiyid Abdul Hai attest to the iconoclasm of Qutb-ud-din Aybak. The first mosque built in Delhi, the "Quwwat al-Islam" was built after the demolition of the Hindu temple built previously by Prithvi Raj and certain parts of the temple were left outside the mosque proper.  This pattern of iconoclasm was common during his reign, although an argument goes that such iconoclasm was motivated more by politics than by religion. 
1. 4. 2. Iltutmish
Another ruler of the sultanate, Shams-ud-din Iltutmish, conquered and subjugated the Hindu pilgrimage site Varanasi in the 11th century and he continued the destruction of Hindu temples and idols that had begun during the first attack in 1194. 
1. 4. 3. Firuz Shah Tughlaq
Firuz Shah Tughluq was the third ruler of the Tughlaq dynasty of the Delhi Sultanate. The "Tarikh-i-Firuz Shah" is a historical record written during his reign that attests to the systematic persecution of Hindus under his rule.  In particular, it records atrocities committed against Hindu Brahmin priests who refused to convert to Islam:
“ An order was accordingly given to the Brahman and was brought before Sultan. The true faith was declared to the Brahman and the right course pointed out. but he refused to accept it. A pile was risen on which the Kaffir with his hands and legs tied was thrown into and the wooden tablet on the top. The pile was lit at two places his head and his feet. The fire first reached him in the feet and drew from him a cry and then fire completely enveloped him. Behold Sultan for his strict adherence to law and rectitude.  ”
Under his rule, Hindus who were forced to pay the mandatory Jizya tax were recorded as infidels, their communities monitored and, if they violated Imperial ordinances and built temples, they were destroyed. In particular, an incident in the village of Gohana in Haryana was recorded in the "Insha-i-Mahry" (another historical record written by Amud Din Abdullah bin Mahru) where Hindus had erected a deity and were arrested, brought to the palace and executed en-masse. 
In 1230, the Hindu King of Orissa Anangabhima III consolidated his rule and proclaimed that an attack on Orissa constituted an attack on the king's god. A sign of Anangabhima's determination to protect Hindu culture is the fact that he named is new capital in Cuttack “Abhinava Varanasi.” His anxieties about further Muslim advances in Orissa proved to be well founded.
1. 5. In the Mughal empire
The Mughal Empire was marked by periods of tolerance of non-Muslims, such as Hindus and Sikhs, as well as periods of violent oppression and persecution of those people.  The reign of Aurangzeb was particularly brutal. No aspect of Aurangzeb's reign is more cited - or more controversial - than the numerous desecrations and even the destruction of Hindu temples.  Aurangzeb banned Diwali, placed a jizya (tax) on non-Muslims and martyred the ninth Sikh guru Tegh Bahadur. 
During his reign, tens of thousands of temples were desecrated: their facades and interiors were defaced and their murtis (divine images) looted.  In many cases, temples were destroyed entirely; in numerous instances mosques were built on their foundations, sometimes using the same stones. Among the temples Aurangzeb destroyed were two that are most sacred to Hindus, in Varanasi and Mathura.  In both cases, he had large mosques built on the sites. 
The Kesava Deo temple in Mathura, marked the place that Hindus believe was the birth place of Shri Krishna.  In 1661 Aurangzeb ordered the demolition of the temple, and constructed the Katra Masjid mosque. Traces of the ancient Hindu temple can be seen from the back of the mosque. Aurangzeb also destroyed what was the most famous temple in Varanasi- the Vishwanath Temple.  The temple had changed its location over the years, but in 1585 Akbar had authorized its location at Gyan Vapi. Aurangzeb ordered its demolition in 1669 and constructed a mosque on the site, whose minarets stand 71 metres above the Ganges. Traces of the old temple can be seen behind the mosque. Centuries later, emotional debate about these wanton acts of cultural desecration continues. Aurangzeb also destroyed the Somnath temple in 1706. 
Hindu nationalists claim that Mughals destroyed the Ram Mandir in Ayodhya, located at the birthplace of Rama, and built the Babri Masjid on the holy site, which has since been a source of tension between the Hindu and Muslim communities.
Writer Fernand Braudel wrote in A History of Civilizations (Penguin 1988/1963, p. 232-236), Islamic rule in India as a "colonial experiment" was "extremely violent", and "the Muslims could not rule the country except by systematic terror. Cruelty was the norm - burnings, summary executions, crucifixions or impalements, inventive tortures. Hindu temples were destroyed to make way for mosques. On occasion there were forced conversions. If ever there were an uprising, it was instantly and savagely repressed: houses were burned, the countryside was laid waste, men were slaughtered and women were taken as slaves."