The pathogenesis of the aberrant development of the male genital tract (epididymis, vas deferens and seminal vesicles) seen in patients with congenital bilateral absence of the vas deferens (CBAVD) is still unclear. Since men with CBAVD carry mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR), it is likely that CFTR mRNA of the translated protein plays a major role in the pathogenesis of CBAVD. The aim of this study was to compare the pattern of expression of CFTR mRNA in epididymides of men with CBAVD and other types of obstruction (post-vasectomy and post-inflammatory) with that of normal non-obstructed adult epididymis. Epididymal biopsies were obtained at the time of microsurgical epididymal sperm aspiration procedures or during vaso-epididymostomy reanastomosis. A normal epididymis was obtained from an orchiectomy specimen. After standard processing for in situ hybridization, tissue sections were hybridized with CFTR gene-probe labelled by incorporation of digoxigenin-dUTP. After hybridization the signal was detected by an alkaline phosphatase-tagged antidigoxigenin antibody. CFTR mRNA was clearly identified in the columnar epithelium of the normal adult epididymis and vas deferens and the signal intensity was greatest in the most proximal regions of the caput epididymis. In contrast, men with genital tract obstructions due to CBAVD or post-vasectomy or post-inflammatory obstructions, had sloughing of the epithelial cells lining the lumen and as a consequence CFTR mRNA expression was lacking. In one subject (post-vasectomy obstruction), some residual caput epididymal epithelium was preserved and CFTR mRNA was detected. The abundant CFTR mRNA expression in the proximal caput of the epididymis and vas deferens under normal conditions strongly favours the hypothesis of an early obstructive process in the pathogenesis of CBAVD. The absent or severely reduced activity of CFTR protein affects the ionic exchange and fluid content within the epididymal lumen and this, in turn, can lead to excessive viscosity of the epididymal fluid, sloughing of epithelial cells expressing CFTR and further reduction in the amount of CFTR activity. As a consequence, variable segments of the epididymis and the vas deferens may be blocked and progressively obliterated. The epididymal lumen obstruction could also sustain the anatomical defects by not allowing testosterone to exert a local action on the mesonephric duct.