MicroRNA-based body fluid identification systems can play a substantial role in forensic casework. Although semen is one of the most important stains in cases of sexual assault, the effect of the absence of spermatozoa in the semen on the efficacy of microRNA-based body fluid identification has not been investigated. In this study, we aimed to investigate the influence of the absence of spermatozoa by determining the expression of candidate microRNAs for in forensically relevant body fluids using RT-qPCR. The expression levels of microRNAs relevant in semen, venous blood, saliva, and vaginal secretion were not significantly different between semen samples with normospermia and azoospermia. We concluded that the absence of spermatozoa did not influence microRNA-based body fluid identification. Therefore, microRNAs can be useful markers in sexual assaults cases, even if the perpetrator is infertile.