Congenital bilateral absence of the vas deferens (CBAVD) is a relatively frequent cause of male infertility accounting for 1-2% of cases of male sterility and at least 6% of cases of obstructive azoospermia. In the last decade a genetic basis for CBAVD has been provided by its association with cystic fibrosis (CF) and nowadays CBAVD is in most cases considered to be a mild or incomplete form of CF disease. Many individuals with CBAVD show usually mild CF-compatible clinical manifestations, but the long-term prognosis could possibly not be as innocuous as it presently looks: more data will be available through medium or long-term follow-up studies. Once a correct diagnosis of CBAVD has been formulated and if the couple is planning a pregnancy by artificial reproductive technology, it is crucial to test both the affected male and his partner for CFTR mutations. Such testing has a number of complex implications and should always be performed together with genetic counselling. Other issues are debated in this article including CF mutations in non-CBAVD forms of male infertility, and the potentially misleading role of CF genetic analysis when used to rule out other possible causes of infertility in azoospermic men.