Objective: The minor histocompatibility antigens (mHAgs) are the epitopes composed of polymorphic essential peptides, and they create T cell response limited to a variety of class I and II HLA alleles. In recent years, there has been extensive research on the distribution of polymorphic regions in different populations. The incompatibility between recipient and donor, may initiate a strong cellular immune response despite HLA full-matched transplantation. We determined the frequency of minor antigens among hematopoietic stem cell transplantation (HSCT) recipients who underwent transplantation for various hematological diseases. Material and Methods: The study population included 200 healthy individuals, 150 HLA-typed patients who were candidates for allogeneic HSCT, and 20 recipients/donors with allogeneic transplants. Minor HAgs identified by using polymerase chain reaction (PCR) and sequence specific primer (SSP) methods. Results: When the allele frequencies and genotypes of the patients were compared with those of the healthy group, the difference was not significant regarding to immunogenic or non-immunogenic allele frequencies. The individuals with immunogenic homozygous H allele (HH genotype) were a few more in the healthy group, and this difference proved to be statistically significant. In fact, our study population Insufficient though the number was, based on the data received from 20 transplant patients and donors, GvHD was observed in 5 of 10 patients who had minor incompatibility. Conclusion: We assume that determining the mHAg frequencies in the healthy Turkish population and in patients with malignant hematological diseases will likely contribute to the understanding of the immune response.