There is an increasing demand to use scanning electron microscopy in the forensic analysis of biological samples. Such analyses are routinely used for the investigation of blood stains, seminal stains, diatoms, residues on wounds and residues and trace elements in gunshot powder. The same samples are sometimes also required for identification via DNA analysis, e.g. blood stains, seminal stains or epidermal cells. The ionising radiation provokes damage to DNA and also to membrane and protein structure. The question therefore arises whether the usual sequence of such an investigation, i.e. prior application of SEM and afterwards analysis of DNA, can affect the success rate of the DNA analysis. We have therefore experimentally exposed semen samples to a defined electron beam for different time intervals varying between 1 and 25 min and afterwards performed quantitative and qualitative DNA analysis. Our studies revealed that sample treatment with an electron beam does not interfere with subsequent DNA typing by various currently used forensic PCR systems.