Purpose To investigate the relationship between sperm apoptotic biomarkers and patient clinical characteristics, conventional sperm parameters and fertility potential. Material and methods Sperm analysis, phospholipid asymmetry, mitochondrial membrane potential (MMP) and DNA denaturation were assessed in 142 males of infertile couples. Seventy-three couples were allocated to the natural conception group, and 55 couples underwent IVF or ICSI. Results DNA denaturation correlated positively with age and negatively with testicular volume (TV). MMP correlated negatively with BMI and FSH and positively with TV. Normal viable sperm correlated positively with TV and negatively with age, BMI and FSH. DNA denaturation was associated with a significantly lower natural pregnancy rate (OR 5.4, p00.011). Conclusion Sperm apoptosis is related to male age, BMI, testicular volume and FSH. Among the apoptotic markers, only DNA denaturation has been found to predict natural pregnancy better than conventional sperm parameters.