The inclusion of apoptotic spermatozoa during assisted reproductive techniques (ART) may be one reason for suboptimal success rates. The aim of our study was to evaluate the potential of routine semen preparation to eliminate spermatozoa with activated apoptosis signalling. Semen samples from 20 infertility patients scheduled for ART procedures were investigated. Following density gradient centrifugation (DGC) and swim‐up, aliquots were taken from each sample to analyse motility, Caspase‐3 activation (CP3) and integrity of the mitochondrial membrane potential (MMP) using flow cytometry. Aliquots from the neat semen served as controls. Semen samples of patients contained 53.8 ± 17.7% spermatozoa with disrupted MMP and 51.8 ± 14.9% with active CP3. Preparation by DGC and swim‐up resulted in improvement of progressive motility (+43.5%) and reduction of spermatozoa with disrupted MMP (−34.3%) and activated CP3 (−25.7%, P < 0.01). Minimal reduction of spermatozoa with disrupted MMP and active CP3 was 6.0% and 0.7%, maximum reduction was 65.5% (disrupted MMP) and 49.3% (CP3). Semen samples of subfertile patients contain high levels of spermatozoa with activated apoptosis signalling. Although there was a reduction in the majority of the samples, profound interindividual differences in the separation effect demand further development of innovative molecular‐based separation methods to deplete apoptotic spermatozoa.