A qualitative diagnosis of infertility requires attention to male and female physical abnormalities including endocrine anomalies and genetic conditions that interfere with reproduction. Many genes are likely to be involved in the complex process of reproduction. Congenital bilateral absence of the vas deferens (CBAVD) is a genital form of cystic fibrosis (CF) that is responsible for 2%-6% of male infertility. The incidence of CF varies in different populations; therefore, the incidence of CBAVD will also vary in different populations. The spectrum and distribution of cystic fibrosis transmembrane conductance regulator (CFTR) gene mutations differ between CBAVD and CF patients and are comparable to control individuals. Combinations of particular alleles at several polymorphic loci yield insufficient functional CFTR protein. CFTR mutations are also associated with congenital absence of the uterus and vagina (CAUV). Females with CF are found to be less fertile than normal healthy women. Because of techniques such as intracytoplasmic sperm injection (ICSI), CBAVD patients are now able to father children. Such couples, however, have an increased risk of having a child with cystic fibrosis, and therefore genetic testing and counseling should be provided. Around 10% of obstructive azoospermia is congenital and due to mutations in the CF gene. This review highlights the relationship of mutations in the CFTR gene with CBAVD and CAUV.