Morphogenetic factors have been shown to play a role in embryogenesis and post-embryonic disease. Interstitial pulmonary fibrosis is a chronic and often progressive disorder that can lead to end-stage cystic lung. Its two major subtypes, usual interstitial pneumonitis (UIP) and nonspecific interstitial pneumonitis (NSIP) differ in their response to immunosuppressive regimens, with UIP having a significantly worse prognosis. The clinical and histologic overlap between these disorders is substantial, and there are no ancillary findings that can accurately distinguish them. We examined surgical and autopsy specimens of lung in 13 cases of patients with either UIP or the fibrotic variant of NSIP (NSIP-F) for their expression of Sonic hedgehog (Shh) and Foxf1 in situ. We identified a pattern of strong Shh expression with weak expression of Foxf1 in all cases of UIP and a complementary expression of Shh and Foxf1 in cases of NSIP-F. We conclude that morphogenetic genes may participate differentially in the pathogenesis of UIP and NSIP-F.