CatSper affects sperm function and male fertilization capacity markers, including sperm motility and egg penetration. The study has aimed to evaluate the mRNA expression of CatSper1, and CatSper3 in the spermatozoa of men with normozoospermia and Asthenoteratozoospermia, and to assess the correlation between genes expression and sperm parameters, fertilization rate, and embryo quality in intracytoplasmic sperm injection (ICSI). Reverse transcription-polymerase chain reaction was utilized to evaluate the mRNA expression of CatSper1 and CatSper3 in sperm in two patient groups: Normozoospermia (NOR; n = 32), and Asthenoteratozoospermia (AT; n = 22). In all patients receiving intracytoplasmic sperm injection, the fertilization rate and embryo quality were evaluated. CatSper1, and CatSper3 mRNA expression in sperm was significantly lower in AT males than in NOR (P < 0.05). Levels of these genes demonstrated a significant positive correlation with sperm motility, mitochondrial membrane potential (MMP), capacitation, fertilization rate, cleavage rate, and embryo quality (P < 0.05) following ICSI. However, a negative correlation was found between mRNA expression of CatSper1, 3 and sperm DNA fragmentation (P < 0.05). Findings indicate low levels of CatSper1 and CatSper3 mRNA expression in men with Asthenoteratozoospermia, which resulted in poor sperm quality and impaired embryo development following ICSI therapy.