Mutations of the cystic fibrosis transmembrane regulator (CFTR) gene and polymorphisms, such as the (TG)m and Tn polymorphic loci in intron 8 at the splice acceptor site of exon 9, can cause male infertility. The aim of this study was to investigate the frequency of the most prevalent cystic-fibrosis-causing mutations, the IVS8-Tn alleles and IVS8-TG12 variant in the presence of IVS8-5T in patients with altered semen parameters (group I with obstructive azoospermia, group II with secretory azoospermia and group III with severe oligozoospermia) compared with a control group with normozoospermia. CFTR mutations were found in 26.5% and 14.3% of chromosomes of patients of group I and II respectively (P < 0.001, P < 0.05). The frequency of the 5T allele was 23.5% in patients in group I (P < 0.01), and was linked exclusively with TG12 allele. The present study reports for the first time a high proportion of the 5T allele in patients in group III (9.2%, P < 0.05). These results underline the importance of performing molecular analysis of mutations and IVS8-Tn polymorphism in the CFTR gene and appropriate genetic counselling to all couples undergoing assisted reproductive technologies when the partner has azoospermia or severe oligozoospermia.