This study evaluated the integrity of the chromatin structure, reactive oxygen species (ROS) levels, mitochondrial membrane potential (MMP), DNA damage and lipid peroxidation of semen samples from infertile men classified as unexplained infertility.Between February 2010 and July 2011 semen parameters and functional tests were evaluated in 10 subjects with proven fertility, 10 that belong to general population and 8 with idiopathic infertility. In addition to the conventional semen analysis, the following unconventional seminal analysis were conducted: evaluation of ROS, MMP, sperm chromatin structure assay (SCSA) by flow cytometry, assessment of sperm membrane lipid peroxidation by spectrophotometry, and alkaline comet assay by electrophoresis.We observed a significant increase (P<.05) in the production of ROS and the fragmentation or sperm DNA damage in the population of infertile men. There were no statistically significant differences (P>.05) in the analysis of sperm membrane integrity between the groups. Moreover, we observed significant correlations (P<.05) between SCSA and comet assay (r=0.86) and the production of intracellular ROS (r=-0.588).The sperm from individuals with idiopathic infertility showed high levels of intracellular ROS and increased levels of DNA fragmentation in the sperm. These results suggest that these two parameters are related to unexplained infertility and therefore have clinical importance as a possible diagnostic and prognostic tool in the evaluation of idiopathic male infertility.