Large percentages of abnormal sperm, termed teratospermia, are associated with poor fertility in cats, many of which are threatened with extinction from their natural habitats. Even normal appearing spermatozoa from felids with teratospermia may have a compromised capacity for motility and fertilization indicating there are factors affecting the fertilization capacity of all sperm regardless of morphology. There was a comparative study conducted using the RNA-Seq approach to identify differentially expressed genes between morphologically normal and abnormal sperm from domestic cates with normospermia and teratospermia to elucidate genes and pathways associated with abnormal sperm function. Normal sperm from cats with teratospermia have a gene expression profile similar to abnormal sperm from males with teratospermia. There was also downregulation of cGMP pathways which may be associated with a lesser sperm motility in ejaculates from males with teratospermia. Kinase phosphorylation pathways also were downregulated in normal spermatozoa from ejaculates of males with teratospermia. Results indicate that analysis of sperm gene expression provides for a more precise assessment of sperm function in semen of cats with teratospermia and facilitates identification of molecular abnormalities that may lead to compromised fertilization capacity.