As important pathogenic factors of male infertility, severe multiple morphological abnormalities of the sperm flagella (MMAF) and nonobstructive azoospermia (NOA) are mostly considered to be of genetic origin. Here, we identified biallelic deleterious variants of CFAP54 from three unrelated men with severe MMAF or NOA. CFAP54 deficiency could cause various morphological and ultrastructural abnormalities in sperm flagella. Furthermore, CFAP54-deficient men could obtain good clinical outcomes after intracytoplasmic sperm injection (ICSI) treatment. In conclusion, this study revealed CFAP54 as a novel gene involved in human male infertility, and provided a vital reference for personalized genetic counselling and ICSI treatment. (By Prof. Feng Zhang, https://jmg.bmj.com/content/early/2023/01/01/jmg-2022-108887 )