Living species including humans are continuously exposed to low levels of a myriad of endocrine active compounds that may affect their reproductive function. In contrast, experimental designs scrutinizing this question mostly consider the gestational/lactational period, select high unrealistic doses and, have rarely investigated the possible reproductive consequences in the progeny. The present study aimed at assessing comparatively a set of male reproductive endpoints according to exposure windows, gestational/lactational versus pre-pubertal to adulthood, using low doses of endocrine active substances in male rats as well as their unexposed male progeny. Animals were orally exposed to 1 mg/kg bw/d of genistein and/or vinclozolin, from conception to weaning or from prepuberty to young adulthood. A number of reproductive endpoints were assessed as well as testicular mRNA expression profiles, in the exposed rats and their unexposed progeny. Overall, the low dosage used only affected weakly most of classical reproductive endpoints. However, the gestational/lactational exposure to vinclozolin alone or combined to genistein significantly delayed the puberty onset. Contrasting with the gestational/lactational exposure, a decreased sperm production was found in the animals exposed to genistein and vinclozolin from the pre-pubertal period but also in their progeny for vinclozolin and the mixture. The expression level of several genes involved in meiosis, apoptosis and steroidogenesis was also affected differentially as a function of the exposure window in both exposed rats and unexposed offspring. We also provide further evidence that doses of endocrine active substances relevant with human exposure may affect the male reproductive phenotype and testicular transcriptome in the exposed generation as well as in the indirectly exposed offspring.