Germ cells constitute the vehicles of genetic information and thereby of inheritance through generations. The epigenetic control mechanisms that govern maintenance and reprogramming of the germline in diverse organisms have gained increasing interest as they reveal essential regulatory pathways implicated in health and disease. We describe a step-by-step transillumination-assisted microdissection method currently used in our laboratory to routinely characterize various spermatogenic cell types. This methodology is ideal to analyze nuclear chromatin condensation and allows further evaluation of epigenetic modifications in male germ cells.