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Abstract Retractions of peer-reviewed biomedical journal articles with Indian authorship have been on the rise for many years. Our study aimed to investigate the reason behind these retractions, namely plagiarism, falsification, fabrication, duplicate publication, author conflicts, ethical issues, fake peer-reviews, and data-related issues, besides providing year-wise trends regarding retraction, authorship, impact factor, and citations. We retrieved retracted publications with Indian affiliations indexed in MEDLINE between 1 January 1990 to 31 December 2021. During this period a total of 619 papers from 372 different journals with median values (interquartile range) pertaining to impact factor [3.2 (1.5, 5.2)], retraction time [24 (10, 51)] months, pre-retraction citations [4 (1, 12)], and post-retraction citations [4 (2, 12)] were retracted. While retractions still account for a small fraction of all publications (0.1%), the overall rate of retractions, that is, the number of retractions relative to the number of newly published journal articles in a given year, has been increasing. The reasons for retractions included plagiarism (27%), falsification and fabrication (26%), duplicate publication (21%), erroneous data (12%), authorship issues (4%), fake-peer reviews (3%), and ethical and funding issues (2%). We have analysed these reasons separately and compared them with each other. Besides a spurt in retraction due to plagiarism, instances of falsification have been escalating over the past decade. Half of the papers retracted on grounds of falsification were published by repeat offender authors in high-impact journals. Furthermore, 82% of retracted papers continued to accumulate citations even after the release of the journal retraction notices. The increase in retractions raises concerns over research quality as well as the wastage of scientific resources, which is especially pressing considering the present environment of scarce funding. The problem of retractions due to reasons such as plagiarism, duplicate publication, authorship issues, and, ethical issues as well as post-retraction citations can be mitigated by educating and raising awareness on publication ethics and responsible research conduct of researchers and journal publishers. Retractions due to fabrication, falsification, and fake peer reviews are more challenging to difficult to address and require further research for the identification of effective solutions.