We investigated whether deranged nitric oxide synthase (NOS) and neuropeptide Y (NPY) expression is detectable in the stenotic segments of patients with congenital ureteropelvic junction obstruction. Using real-time reverse transcription-polymerase chain reaction (RT-PCR), we quantified mRNA amounts of NPY, neuronal (n), endothelial (e) and inducible (i) NOS in the stenotic segments of 20 patients with congenital ureteropelvic junction obstruction (aged 5.1+/-7.0 years) and of 21 unaffected controls (aged 23.5+/-24.2 years). Additionally, mRNAs of glyceraldehyde-3-phosphate dehydrogenase (GAPDH), smooth muscle alpha-actin (Smactin), endothelial cell marker (CD31), and protein gene product 9.5 (PGP 9.5) were evaluated. Immunohistochemistry was made for NPY, nNOS, eNOS, iNOS, PGP 9.5, and CD 31. The mRNA of nNOS was significantly reduced in the obstructed junctions when related to the mRNAs of Smactin (P < 0.001) or GAPDH (P < 0.05), respectively. A significant reduction was also obtained for eNOS mRNA when standardized to CD31 (P < 0.05), GAPDH or Smactin mRNA (P < 0.05, and P < 0.001, respectively). NPY, PGP 9.5 and iNOS mRNAs were found in comparable quantities in both groups. In the stenotic segments, Smactin mRNA level was about twofold higher than in our control specimens, as shown by the lower CT values for the patients in real-time PCR (16.9+/-2.0 vs 17.9+/-2.6, P < 0.05). Furthermore, Smactin, nNOS, iNOS, eNOS, and NPY mRNA levels in specimens of unaffected ureteropelvic junctions were independent of age. Major differences between control and stenotic tissues were detected by immunohistochemistry: There was a dramatic reduction of innervation density as evidenced by nNOS and NPY labeling. Taken together, we found alterations in NOS gene expression and NPY innervation in tissue specimens of patients with congenital ureteropelvic junction obstruction.