ABSTRACT: Introduction:The purpose of this study was to investigate the correlation between sperm mitochondrial NADH dehydrogenase subunit 5 (ND5) and NADH dehydrogenase subunit 6 (ND6) gene variations and total fertilisation failure (TFF). Material and methods:A total of 232 sperm samples at the fresh in vitro fertilisation (IVF) cycle or the half-intracytoplasmic sperm injection (ICSI) cycle were collected for this retrospective controlled study on Han Chinese people between July 2011 and April 2014. Of the 232 total samples, 45 were from the IVF-TFF group and 187 were from couples with normal fertilisation (fertilisation rate > 50%). The mitochondrial ND5 and ND6 gene variations and sperm haplotypes were confirmed using nested PCR and DNA sequencing. Results:Ten homozygous variations were newly discovered, namely C12417T, T12441A, C12543A, C13650A, C13765A, T13769C, C13775T, A13776G, C13785A and C13845T. The gene variation rates of six sites, C12417T, C13650A, C13765A, T13769C, C13785A and C13845T, in the TFF group were significantly higher than those in the control group (p < 0.05). There were 231 heterozygous variations discovered; however, only nine heterozygous sites (12441, 12561, 12735, 13164, 13743, 13812, 13928, 14172 and 14368) had significantly higher gene variation rates than those in the control group (p < 0.05). In addition, the results showed that haplogroup C did not affect TFF (p > 0.05), and the fertilisation failure rates of haplogroup R and haplogroup D4a were both higher than those in the control group (p < 0.05). Conclusions:Our results suggested that the ND5 and ND6 gene variations are correlated with TFF. Furthermore, this study indicated that haplogroup R and haplogroup D4a might be risk factors for TFF.