Asthenozoospermia is a common cause of male infertility, which is characterized by reduced forward motility of spermatozoa. The cause and pathogenesis of asthenozoospermia are not fully understood. The purpose of this study was to investigate the expression of nicotinamide adenine dinucleotide (NADH) dehydrogenase (ubiquinone) 1 alpha subcomplex, 13 (NDUFA13) in the spermatozoa of men with asthenozoospermia and its possible pathogenesis. Protein content of NDUFA13 in spermatozoa was measured by Western blot analysis. The results showed that NDUFA13 expression in spermatozoa was significantly lower in men with asthenozoospermic than in men with normozoospermia (P < 0.01). Immunofluorescence experiments showed that NDUFA13 was expressed predominantly in the sperm mid-piece. A lower mitochondrial membrane potential, a higher intracellular reactive oxygen species (ROS) level and more apoptotic cells were also detected in men with asthenozoospermia. NDUFA13-specific small interfering RNA was used in the mouse spermatocyte GC2-spd cell line to down-regulate the expression of NDUFA13. The knockdown of NDUFA13 in the GC2-spd cells caused a collapse of mitochondrial membrane potential, an increase in ROS level and more apoptotic cells. Our study showed that NDUFA13 deficiency may be associated with asthenozoospermia through the disturbance of spermatozoa mitochondrial membrane potential and by increasing apoptosis and intracellular ROS.