1. 6. Haidar Ali and Tipu Sultan
The attitudes of Muslim ruler Tippu Sultan have been criticized as anti-Hindu. While some Marxist historians claim that he had an egalitarian attitude towards Hindus and was harsh towards them only when politically expedient,  In the first part of his reign in particular he appears to have been notably more aggressive and religiously doctrinaire than his father, Haidar Ali.  There are some historians  who claim that Tippu Sultan was a religious persecutor of Hindus.
C. K. Kareem also notes that Tippu Sultan issued an edict for the destruction of Hindu temples in Kerala. 
Historian Hayavadana C. Rao wrote about Tippu in his encyclopaedic work on the History of Mysore. He asserted that Tippu's "religious fanaticism and the excesses committed in the name of religion, both in Mysore and in the provinces, stand condemned for all time. His bigotry, indeed, was so great that it precluded all ideas of toleration". He further asserts that the acts of Tippu that were constructive towards Hindus were largely political and ostentatious rather than an indication of genuine tolerance. 
Hindu groups revile Tipu Sultan as a bigot who massacred Hindus.  He was known to carry out forced conversions of Hindus and Christians.  [Need quotation to verify]. According to Ramchandra Rao "Punganuri" Tipu converted 500 Hindus in Kodagu (Coorg). 
However this view must be contrasted against evidence that he corresponded with the Sringeri Shankaracharya - expressing grief and indignation at a raid by Maratha horsemen, which killed many and plundered the monastery of its valuable possessions 
B.A. Saletare has described Tipu Sultan as a defender of the Hindu dharma. He is praised for patronizing the Melkote temple , for which he issued a Kannada decree that the Shrivaishnava invocatory verses there should be recited in the traditional form. The temple at Melkote still has gold and silver vessels with inscriptions indicating that they were presented by the Sultan. Tipu Sultan also presented four silver cups to the Lakshmikanta Temple at Kalale.  There appears to be some evidence that he presented the Ranganatha temple at Srirangapatana with seven silver cups and a silver camphor burner. This temple was hardly a stone's throw from his palace from where he would listen to both the ringing of temple bells and the muezzin's call from the mosque. 
Some historians have argued that these acts happened after the Third Mysore war, where he had to negotiate on the terms of surrender. They claim that these acts could have been motivated by a political desire to get the support of his Hindu subjects.
1. 7. In Kashmir
The Hindu minority in Kashmir has also been historically persecuted by Muslim rulers.  While Hindus and Muslims lived in harmony for certain periods of time, several Muslim rulers of Kashmir were intolerant of other religions. Sultãn Sikandar Butshikan of Kashmir (AD 1389-1413) is often considered the worst of these. Historians have recorded many of his atrocities. The Tarikh-i-Firishta The 2000 Amarnath pilgrimage massacre was another incident where 30 Hindu pilgrims were killed on route to Amarnath temple.
 Even now these continue by majority Muslim community there on indigenous Hindus.  records that Sikandar persecuted the Hindus and issued orders proscribing the residency of any other than Muslims in Kashmir. He also ordered the breaking of all "golden and silver images". The Tarikh-i-Firishta further states: "Many of the Brahmins, rather than abandon their religion or their country, poisoned themselves; some emigrated from their native homes, while a few escaped the evil of banishment by becoming Mahomedans. After the emigration of the Bramins, Sikundur ordered all the temples in Kashmeer to be thrown down. Having broken all the images in Kashmeer, (Sikandar) acquired the title of ‘Destroyer of Idols’".
2. During European rule of the Indian subcontinent
2. 1. Goa
Main article: Goa Inquisition
The Goa Inquisition, was established in 1560 by Portuguese missionaries. It was aimed primarily at Hindus and wayward new converts and by the time it was suppressed in 1774, the inquisition had had thousands of Hindus tortured and executed by burning. The British East India Company engaged in a covert and well-financed campaign of evangelical conversions in the 19th century. While officially discouraging conversions, officers of the Company routinely converted Sepoys to Christianity, often by force. This was one of the factors that led to the First Indian War of Independence. 
3. During the era of Nizam state of Hyderabad
Hindus were severely repressed under the autocratic dictatorial rule of the Nizam nawabs in Hyderabad state. The Hindu majority were denied fundamental rights by the Nizams of Hyderabad state. Hindus were called gaddaar (traitor) by Muslims in the Nizam state of Hyderabad.  Many Hindus were murdered, looted and thrown to jail. Construction of temples were declared illegal and Hindu scriptures like Bhagavad Gita, Ramayana were banned. 
Hindus were treated as second class citizens within Hyderabad state and they were severely discriminated against, despite the vast majority of the population being Hindu. The 1941 census estimated the population of Hyderabad to be 16.34 million. Over 85% of the populace were Hindus with Muslims accounting for about 12%. Hyderabad was also a multi-lingual state consisting of peoples speaking Telugu (48.2%), Marathi (26.4%), Kannada (12.3%) and Urdu (10.3%). Nonetheless, the number of Hindus in government positions was disproportionately small. Of 1765 officers, 1268 were Muslims, 421 were Hindus, and 121 were "Others" (presumably British Christians, Parsis and Sikhs). Of the officials drawing pay between Rs.600-1200 pm, 59 were Muslims, 38 were "Others", and a mere 5 were Hindus. The Nizam and his nobles, who were mostly Muslims, owned 40% of the total land in the kingdom. 
In 1947; Nizam, the ruler of Hyderabad refused to merge his kingdom with India. For the independence of the Islamic state of Hyderabad and to resist Indian integration, All India Majlis-e-Ittehadul Muslimeen, the then dominating political party persecuted Hindus and their 1,50,000 cadre strong militant wing named Razakars killed a number of Hindus under the leadership of Qasim Rizwi. 
4. Contemporary persecution
While the vast majority of Hindus live in Hindu-majority areas of India, Hindus in other parts of South Asia and in the diaspora have sometimes faced persecution.
4. 1. In the Indian subcontinent
4. 1. 1. Republic of India
Although the Indian government allows for freedom of religion, its constitution provides lesser rights and protection to Hindus vs. non-Hindus paving way for government confiscation of Hindu institutes and places of worship. More-over, Minority institutes also receive government patronage in form of Exemption from 2005 Amendment to the Article 15, 95% grant-in-aid, College Scholarship to pursue higher education.    
What makes matters worse is that ruling political parties often subscribe to ideologies which are inherently hostile or prejudiced towards Hinduism. Thus, Hindu temples and institutes live under constant threat of ideologically motivated government take-over and subsequent destruction. For instance, State of Tamil Nadu is ruled by Dravidian parties for over two decades. Dravidian ideology believes in discredited racial theory of Aryan Invasion. It is openly anti Shri Ram, anti Sanskrit and anti Brahmin. Ruling ideology has a history of publicly issuing threats and has carried out those threats in many instances.    At some junctures, interpretation of the laws has also disadvantaged Hindus 
Many organizations feel that Hindu label is a liability. It exposes them to ideologically inspired attacks, places them at a financial disadvantage and paves way for government confiscation. As a result, several entities like Rama-Krishna Mission, Arya Samaj, etc. have filed law-suits and done intense lobbying to declare them self a non-Hindu minority religion. For Instance, in west Bengal, Rama Krishna Mission whose colleges and schools were in danger of hostile take-over by Marxist government petitioned the courts to have their organization and movement declared a non-Hindu minority religion.    
Hindus from other countries hoping to come to India have also been treated unfavorably by the Indian government 
Recently the issue of Love Jihad created huge controversy in Southern India, although similar incidents were ignored in Northern India.
4. 1. 1. 1. Jammu and Kashmir
Kashmiri militants have engaged in attacks on Hindu pilgrims in both Kashmir and neighboring Jammu. Kashmiri militants have attacked Hindus in the region, as well as moderate Muslims suspected of siding with India. Kashmiri Pandit Hindus, who have been residents of Kashmir for centuries, have been ethnically cleansed from Kashmir by Islamic militants.   In particular, the Wandhama Massacre in 1998 was an incident in which 24 Kashmiri Hindus were gunned down by Islamists disguised as Indian soldiers. Many Kashmiri Hindus have been killed and thousands of children orphaned over the course of the conflict in Kashmir.
4. 1. 1. 2. Northeast India
In Northeastern India, especially in Nagaland, Hindus are not able to celebrate Durga Puja and other essential festivals due to harassment and killing by Christian terrorist groups. In Tripura,  the NLFT, "National Liberation Front of Tripura", has targeted Swamis and temples for attacks. They are known to have forcefully converted Hindus to Christianity.   The Baptist Church of Tripura is alleged to have supplied the NLFT with arms and financial support and to have encouraged the murder of Hindus, particularly infants. 
In Assam, members of the primarily Christian Hmar ethnic group have placed bloodstained crosses in temples and forced Hindus to convert at gunpoint. 
4. 1. 1. 3. Punjab
Main article: Punjab insurgency
The period of insurgency in Punjab around Operation Bluestar saw clashes of the Sikh militants with the police, as well as with the Hindu-Nirankari groups resulting in many Hindu deaths. In 1987, 32 Hindus were pulled out of a bus and shot, near Lalru in Punjab by Sikh militants. 
4. 1. 1. 4. Kerala
Kerala is a Hindu majority state but with the most slim majority in India.  Kerala has witnessed many riots and rebellions against Hindus throughout it history and more so in independent India; notably the Marad Massacre. Many Muslim organizations allegedly supported Love Jihad where Muslim boys targeted non-Muslim young girls, especially Hindu girls to convert them to Islam by feigning love. 
See also: Hinduism in India
4. 1. 2. Bangladesh
The HAF report documents the long history of anti-Hindu atrocities  in Bangladesh,  a topic that many Indians and Indian governments over the years have preferred not to acknowledge. Such atrocities, including targeted attacks  against temples, open theft of Hindu property, and rape of young Hindu women and enticements to convert to Islam, have increased sharply in recent years after the Jamat-e-Islami joined the coalition government led by the Bangladesh National Party.  
Bangladesh has had a troublesome history of persecution of Hindus as well. A US-based human rights organisation, Refugees International, has claimed that religious minorities, especially Hindus, still face discrimination in Bangladesh.  The government of Bangladesh, a nationalist party openly calls for ‘Talibanisation’ of the state.    However, the prospect of actually "Talibanizing" the state is regarded as a remote possibility, since Bangladeshi Islamic society is generally more progressive than the extremist Taliban of Afghanistan. Political scholars conclude that while the Islamization of Bangladesh is real, the country is not on the brink of being Talibanized.  In 1971 at the time of the liberation of Bangladesh from East Pakistan, the Hindu population accounted for 15% of the total population. Thirty years on, it is now estimated at just 10.5%.  The ‘Vested Property Act’ previously named the ‘Enemy Property Act’ has seen up to 40% of Hindu land snatched away forcibly. Since this government has come into power, of all the rape crimes registered in Bangladesh, 98% have been registered by Hindu women. Hindu temples in Bangladesh have also been vandalised.   The United States Congressional Caucus on India has condemned these atrocities. 
Bangladeshi feminist Taslima Nasrin's 1993 novel Lajja deals with the anti-Hindu riots and anti-secular sentiment in Bangladesh in the wake of the destruction of the Babri Masjid in India. The book was banned in Bangladesh, and helped draw international attention to the situation of the Bangladeshi Hindu minority.
In October 2006, the United States Commission on International Religious Freedom published a report titled 'Policy Focus on Bangladesh', which said that since its last election, 'Bangladesh has experienced growing violence by religious extremists, intensifying concerns expressed by the countries religious minorities'. The report further stated that Hindus are particularly vulnerable in a period of rising violence and extremism, whether motivated by religious, political or criminal factors, or some combination. The report noted that Hindus had multiple disadvantages against them in Bangladesh, such as perceptions of dual loyalty with respect to India and religious beliefs that are not tolerated by the politically dominant Islamic Fundamentalists of the Bangladesh Nationalist Party. Violence against Hindus has taken place "in order to encourage them to flee in order to seize their property".The previous reports of the Hindu American Foundation were acknowledged and confirmed by this non-partisan report. 
On November 2, 2006, USCIRF criticized Bangladesh for its continuing persecution of minority Hindus. It also urged the Bush administration to get Dhaka to ensure protection of religious freedom and minority rights before Bangladesh's next national elections in January 2007. 
On the February 6, 2010, Sonargaon temple in Narayanganj district of Bangladesh was destroyed by Islamic fanatics. Five people were seriously injured during the attack.