BACKGROUND: The purpose of this study was to identify morphological differences on the computed tomographic (CT) scan between cryptogenic fibrosing alveolitis (CFA) and the fibrosing alveolitis associated with systemic sclerosis (FASSc), and to examine their biological relevance. METHODS: One hundred and seven patients with CFA (n = 55) or FASSc (n = 52) who had undergone thin section CT scanning were included. Multivariate analysis was used to identify morphological differences on the CT scans between lone CFA and FASSc, and to determine whether the pattern and distribution of disease on the CT scans were functionally significant (as judged by the lung transfer factor (TLCO), forced vital capacity (FVC), and arterial oxygen tension (PaO2)) or predictive of survival (independent of the type and extent of fibrosing alveolitis, age, sex, and smoking history). RESULTS: Increasingly extensive disease on CT scans was associated with a coarser reticular pattern (increase in reticular score per percentage increase in disease extent = 0.06, 95% confidence interval (CI) 0.03 to 0.09, p < 0.0005) and increasing upper zone involvement (increase in ratio of upper zone to total disease per percentage increase in disease extent = 0.002, 95% CI 0.000 to 0.003, p < 0.04). Patients with CFA were characterised by a higher upper zone ratio (difference = 0.08, 95% CI 0.02 to 0.13, p < 0.004) and a weak trend towards a coarser reticular pattern (p = 0.09), independent of disease extent. Smokers with CFA had more upper zone involvement (difference = 0.11, 95% CI 0.05 to 0.16, p < 0.0005) and a coarser reticular pattern (difference in reticular score = 1.92, 95% CI 0.27 to 3.55, p < 0.02) than smokers with FASSc. The extent of disease on the CT scan was predictive of lung function impairment and survival but the pattern and distribution of disease were not. CONCLUSIONS: Patients with CFA have relatively more upper zone involvement than those with FASSc independent of the extent of disease on the CT scan. This finding may result from smoking related damage but is not functionally significant.