Background & Aims: The most significant cause of infertility in men is the genetic deletion in the azoospermia factor (AZF) region that is caused by the process of intra- and inter-chromosomal homologous recombination in amplicons. Homologous recombination could also result in partial deletions in AZF region. The aim of this research was to determine the association between the partial AZFc deletions and infertility. Methods: The blood samples were taken from 100 infertile men‚ who referred to the Infertility Center of Isfahan‚ Iran. 100 healthy matched people were also selected as the control group. The five markers of sY1201‚ sY1206‚ sY1161‚ sY1291, and sY1191 were applied in order to study partial deletions. Partial deletions were analyzed in AZF region using the Multiplex–STS–PCR technique. The chi-square test was conducted to check the difference between pretest and posttest. Differences were considered significant if P < 0.05. Results: 9% of studied persons showed gr/gr deletion (in the patient group). Only one case of gr/gr deletion was observed in the control group. Five patients showed b2/b3 deletion. One b2/b3 deletion was seen in the control group. The b2/b4 deletion was observed in 3 patients. In conclusion‚ partial deletions were observed in 14% of the patients. The statistical analysis of the gr/gr deletion in the study indicates a meaningful difference, but b2/b3 deletion does not represent a meaningful difference. Conclusion: Our results suggest that gr/gr deletions are associated with spermatogenic failure, and there is no association between b2/b3 deletion and infertility