Costimulatory molecules are important factors determining the outcome of bone marrow transplant. Because the host ability in costimulatory molecule function may be affected by gene polymorphisms, the aim of the present study was to investigate the effect of CTLA4, ICOS, PD.1 and CD28 gene polymorphisms in outcome of bone marrow transplant patients. A total of 72 recipients were included in this study. CTLA4 (-1722, -1661, -318, +49), ICOS (+1720), CD28 (+17) and PD.1 (PD.1.3, PD.1.9) gene polymorphisms were evaluated by PCR-RFLP. The results showed that no differences in the distribution of all mentioned costimulatory molecules genotypes and alleles were observed in the Graft Versus Host Disease (GVHD) group compared to the non-GVHD group. After gender classification, there is a significant association between GA genotype (CTLA4-1661) in male group with GVHD than without GVHD (p=0.03). Also, in this study we found significant associations between CC genotype and C allele of PD.1.9, and TT genotype and T allele of CD28 that had more frequency in grades 2-4 (p=0.04. p=0.02, p=0.01, p=0.003, respectively). Results indicate that the CC genotype and C allele of PD.1.9 and TT genotype and the T allele of CD28 are genetic risk factors for development of a severe grade of GVHD. This subject needs to be studied in different population.