Introduction: Spermatozoa from infertile men often have multiple structural and functional defects. Sperm DNA damage is one of these defects that may result from DNA fragmentation, abnormal chromatin packaging, and epigenetic defects. In this study the effect of sperm DNA damages on Assisted Reproductive Technology (ART) outcome is investigated.Materials and Methods: This study is an experimental research. Semen samples were obtained from 92 couples referred to Isfahan Fertility and Infertility Center for Intra Cytoplasmic Sperm Injection (ICSI) and In Vitro Fertilization (IVF) treatment. Samples were examined for concentration, morphology and motility according to the WHO guidelines. Semen samples were processed for routine ICSI and IVF using discontinuous Pure Sperm Gradients. After insemination of oocytes, the remaining semen samples were used for evaluation of global DNA methylation, protamine deficiency, and DNA fragmentation using immunostaining, Chromomycin A3 )CMA3) and Sperm Chromatin Dispersion (SCD) test. Data was analyzed using descriptive statistics, t-test and correlation coefficient.Results: The percentage of CMA3 showed a significant positive correlation with percentage of normal morphology, DNA fragmentation and fertilization rate (p<0.05). However, no correlation was found between sperm normal morphology and global DNA methylation. In addition, percentage of DNA fragmentation showed a significant negative correlation with fertilization rate in ICSI patients (p= 0.03), percentage of normal morphology and global DNA methylation. However, this parameter did not significantly affect fertilization rate in IVF patients. During this study, analyzing the relation between protamine deficiency, global DNA methylation and DNA fragmentation with cleavage, embryo quality score and pregnancy was done. No significant correlations were observed between these parameters.Conclusion: Semen samples are heterogeneous population, and may contain sperm with different defects. Sperm defects such as protamine deficiency DNA fragmentation, which was assessed during this study, may affect fertilization but does not affect subsequent development and pregnancy. However, effect of these defects on future of ART children awaits further research.