Biomarkers in germ cells have the same function as in somatic cells; that is, to give an indication of immediate changes at the genomic, transcriptional and translational levels in the cell itself and the potential transmission of some of these alterations to the offspring. There are various types of genetic change which can be detected in germ cells. These include aberrations at the chromosomal as well as the nucleotide level. The cytogenetic aberrations in male and female germ cells in all the stages of spermatogenesis and oogenesis include numerical abnormalities such as aneuploidy and structural aberrations. There are many methodologies representing biomarkers in spermatozoa, such as the in vivo and in vitro Comet assay as well as flow cytometric techniques to detect DNA integrity, fluorescence in-situ hybridization (FISH) for numerical and structural aberrations, DNA-adduct detection via immunological or ³²P post-labelling methods, mRNA profiles, mutation detection at expanded tandem repeat (ESTR) and minisattelite loci, or heritable chromosome assays (for spermatocytes). There are also different methodologies representing biomarkers in oocytes, such as FISH, comparative genomic hybridization (CGH) and the Comet assay, as well as analysis of gene and protein expression. Thus, there are many biomarkers currently available in male and female germ cells. Some are better established than others and some are newly developing. They show great promise for future research and have relevance for clinical use.