This review aims to give an overview of some of the biomarkers that have been used for the monitoring of human exposure to xenobiotics as well as to provide a summary of some of the recent epidemiological studies on male reproductive health of exposure to environmental and occupational toxicants. Possible molecular mechanisms on seminal quality change are also suggested. Studies using various biomarkers have no doubt enabled us to better characterize the effect of environmental pollutants on the male reproductive system. However, the sensitivity and specificity of these biomarkers have not been comprehensively validated. Furthermore, many epidemiological findings are difficult to replicate owing to the inherited methodological problems of male reproductive health investigations, such as the small number of study subjects, low compliance rate, substantial intra-individual variability in semen parameters, measurement techniques and misclassifications based on single assay. Oxidative damage, in particular DNA-damage caused by free radicals, generated either by xenobiotics, or endogenously, is now thought to be a key molecular mechanism associated with semen quality and sperm function. Laboratory studies and epidemiological findings have suggested that the male reproductive system is susceptible to reactive oxygen species (ROS). On the other hand, there is so far no single all-encompassing biomarker of reproductive capacity in men. A panel of biomarkers with specific goals should be considered. Collaborative multidisciplinary studies are also needed to overcome some of the issues mentioned here.