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Shia in South Asia faced persecution by some Sunni rulers and Mughal Emperors which resulted in the killings of Shia scholars like Qazi Nurullah Shustari (also known as Shaheed-e-Thaalis, the third Martyr) and Mirza Muhammad Kamil Dehlavi (also known as Shaheed-e- Rabay, the fourth Martyr) who are two of the five martyrs of Shia Islam. Shias in Kashmir in subsequent years had to pass through the most atrocious period of their history. Plunder, loot and massacres which came to be known as Taarajs virtually devastated the community. History records 10 such Taarajs also known as Taraj-e-Shia between 15th to 19th century in 1548, 1585, 1635, 1686, 1719, 1741, 1762, 1801, 1830, 1872 during which the Shia habitations were plundered, people slaughtered, libraries burnt and their sacred sites desecrated.

Sunni–Shia clashes also occurred frequently in the 20th century in South Asia. There were many between 1904 and 1908 especially in the United Provinces (Uttar Pradesh) area. These clashes revolved around the public cursing of the first three caliphs by Shias and the praising of them by Sunnis. To put a stop to the violence public demonstrations were banned in 1909 on the three most sensitive days: Ashura, Chehlum and Ali's death on 21 Ramadan. Intercommunal violence resurfaced in 1935-6 and again in 1939 when many thousands of Sunni and Shias defied the ban on public demonstrations and took to the streets. Shia are estimated to be 21-35% of the Muslim population in South Asia, although the total number is difficult to estimate due to the intermingling between the two groups and practice of taqiyya by Shia