BACKGROUND: The huge diversity of Human Leukocyte Antigen (HLA) system is well-known to be associated with various diseases, anthropology, population genetics, and transplantation. The frequencies of HLA alleles in different populations are crucial for both research and clinical applications. This study determined the allelic and haplotype frequencies of all HLA class I and class II loci in 595 consecutive samples from patients who underwent solid organ transplantation (SOT) and hematopoietic progenitor cell transplantation (HPCT). METHOD: High-resolution HLA typing for HLA-A, B, C, DRB1, and DQB1 was conducted using a next generation sequencing (NGS) platform. RESULTS: The most frequent alleles observed among all HLAs were A*11:01:01 (0.1849), A*24:02:01 (0.1202) and A*01:01:01 (0.1143) in A locus, B*40:06:01 (0.1050), B*52:01:01 (0.0950) and B*51:01:01 (0.0723) in B locus, C*07:02:01 (0.1303), C*04:01:01 (0.1227) and C*15:02:01 (0.1185) in C locus, DRB1*07:01:01 (0.1286), DRB1*15:01:01 (0.1134) and DRB1*03:01:01 (0.0966) in DRB1 locus, and DQB1*06:01:01 (0.1849), DQB1*03:01:01 (0.1471) and DQB1*02:02:01 (0.0966) in DQB1 locus. The most frequent (>
2 %) five-locus A ∼ B ∼ C ∼ DRB1 ∼ DQB1 haplotypes were A*33:03:01 ∼ B*44:03:02 ∼ C*07:06:01 ∼ DQB1*02:02:01 ∼ DRB1*07:01:01 (2.97 %), A*26:01:01 ∼ B*08:01:01 ∼ C*07:02:01 ∼ DQB1*02:01:01 ∼ DRB1*03:01:01 (2.23 %) and A*02:11:01 ∼ B*40:06:01 ∼ C*15:02:01 ∼ DQB1*06:01:01 ∼ DRB1*15:01:01(2.15 %). Among all tested loci, the HLA-B locus had the most polymorphism, whereas the HLA-DQB1 locus had the least polymorphism. CONCLUSION: The data represent the distribution of HLA-A, B, C, DRB1, DQB1 alleles and their haplotype frequencies among the population in India.