As a highly specialized and evolutionarily conserved organelle, sperm flagellum provides the motile force for delivering the sperm to the egg. Fibrous sheath (FS), located in the principal piece of sperm flagella, serves as mechanical support for flagellar bending. Here, we identified two asthenoteratozoospermia-affected men carrying homozygous variants in AKAP3, encoding a FS associated protein. The deficiency of AKAP3 leading to various morphological abnormalities in sperm flagella accompanied by partial acrosomal abnormalities. Furthermore, different ICSI outcomes were observed in men harbouring AKAP3 variants with different pathogenicity. In conclusion, our study revealed AKAP3 as a novel gene involved in human asthenoteratozoospermia. (By Prof. Feng Zhang, https://jmg.bmj.com/content/early/2022/02/27/jmedgenet-2021-108271 )