BACKGROUND: An increase in the frequency of disorders of the male human reproductive organs has been described over recent decades. Neither its causes nor its consequences on fecundity, the ability of the couples to produce a live child, are clearly known. This lack of knowledge may partly be due to methodological difficulties specific to reproductive epidemiology. METHODS: We discuss the relevance and limits of some markers of the male aspects of human reproduction, focusing on semen parameters and fecundability, a measure of the probability of pregnancy. RESULTS: Semen parameters are associated with fecundability, although they have a relatively low sensitivity to detect couples with low fecundability. The study of semen parameters proved central to describe the influence of environmental factors on the male side of reproductive function. The main limitation of semen studies is low participation rates and the possible selection biases ensuing. Fecundability can be estimated by collecting waiting time to pregnancy. Its assessment in retrospective studies often excludes the least fecund, those couples remaining childless, which entails a bias and a decrease in statistical power. The prospective approach and an approach relying on the enrollment of a cross-sectional sample of the couples currently trying to obtain a pregnancy (current duration approach) do not have these limitations. Although it has never been used, the assessment of fecundability using the current duration approach is promising both for aetiologic research and monitoring. CONCLUSION: Most of the potential markers of male reproductive function are not assessed in the general population of France, with the exception of the incidence rate of testis cancer, which is currently increasing. We present some alternatives for a monitoring system of reproductive function.