Abstract To elucidate the effects of inflammation on sperm quality, this study analysed classical sperm characteristics, leukocytes and elastase in neat semen, and sperm apoptotic markers, i.e. changes in plasma membrane phospholipid asymmetry, mitochondrial membrane potential (MMP), DNA integrity and intracellular reactive oxygen species (ROS), in semen prepared by density gradient using flow cytometry from 348 men of infertile couples. Increased leukocytes (⩾0.1 × 106 /ml) were associated with a decreased sperm concentration, motility and normal morphology ( P ⩽ 0.001). Sperm necrosis and DNA denaturation were increased (31.3 versus 26.6%, P = 0.020; 15.5 versus 11.5%, P = 0.011, respectively), whereas spermatozoa with normal MMP were decreased (64.1 versus 70.0%, P = 0.004). High leukocyte levels (⩾1 × 106 /ml) were not associated with any of the observed sperm parameters. At low elastase concentration (100–290 μg/l), DNA denaturation was higher (16.1 versus 10.5%, P = 0.024) compared with very low elastase concentration (<100 μg/l). A high elastase concentration (290–1000 μg/l) was associated with higher ROS index compared with low elastase concentration (1.28 versus 1.01, P = 0.016). Slightly increased leukocytes and elastase are associated with slightly poorer sperm characteristics and/or increased sperm necrosis, DNA denaturation and intracellular ROS and decreased MMP.