Intracytoplasmic sperm injection (ICSI) has made irrelevant the conventional criteria of concentration, motility and morphology for assessment of sperm quality and so we urgently need new assays by which to gauge sperm 'health'. ICSI may be facilitating the transfer of genetic disorders to future generations by bypassing all the natural hurdles for sperm selection without imposing more pertinent criteria of selection. Sperm DNA quality is vital to the future offspring irrespective of whether the child is conceived naturally, by in vitro fertilization (IVF) or by ICSI. The DNA integrity of sperm can be determined quickly and accurately using a range of techniques that also have strong prognostic power in predicting successful IVF and ICSI outcomes with ejaculated sperm. Moreover, there is a close correlation between testicular nuclear DNA integrity and pregnancy rates in ICSI. Mitochondrial DNA can be measured using long PCR in ejaculated and testicular sperm and is also useful for predicting success in assisted conception. This review discusses how the integrity of both nuclear and mitochondrial affect the choice of sperm for assisted conception.