<p>Background: Microdeletions of the Y chromosome are one of the most frequent genetic causes of spermatogenic failure in infertile men. But their role in gaining weight is unclear. The present study investigated the possible association of these partial microdeletions and obesity.<br /> Methods: In a case-control study, 180 males were selected. The prevalence of microdeletions was assessed using PCR in AZFc area of Y chromosome and statistical analysis was done using the Fisher exact test and Pearson correlation.<br /> Results: In our study, inverse relationship was observed between body mass index and testosterone level (p-value: 0.005). Fisher exact tests showed that there was a significant association between gr/gr mutation and BMI (p-value: 0.044).<br /> Conclusion: Our study revealed that Y chromosome microdeletions are more common in obese men. Furthermore, microdeletions such as gr/gr, which were observed in normal men, could cause decreased testosterone level. So, they may contribute to gaining weight.</p>