OBJECTIVE. The relationship between morphologic alterations of pulmonary small vessels and pulmonary perfusion has not been clarified. The purpose of this study was to evaluate the relationship between the cross-sectional area (CSA) of pulmonary small vessels alterations measured on CT images and pulmonary perfusion on lung perfusion scintigraphy. MATERIALS AND METHODS. This study comprised 46 subjects who underwent both CT and lung perfusion scintigraphy. We measured CSA of pulmonary small vessels less than 5 mm(2) and 5-10 mm(2) using CT images and obtained the percentage of the right lung to whole lung in each CSA group (CSA<5,R/W and CSA5-10,R/W, respectively). Using (99m)Tc-macroaggregated albumin (MAA) lung perfusion scintigraphy, we obtained right and total lung counts and calculated the percentage of the right to whole-lung counts (MAAR/W). Those CT and scintigraphy measurements were also calculated separately each in right upper, right lower, left upper, and left lower zones. The correlations of CSA<5,R/W and CSA5-10,R/W with MAAR/W, the correlation between the percentage of each lung zone to whole-lung CSA<5 and the percentage of each corresponding lung zone to whole-lung MAA were evaluated. RESULTS. The mean CSA<5,R/W was 58.1% ± 11.2%, and the mean MAAR/W was 59.3% ± 17.9%. CSA<5,R/W had a significant correlation with MAAR/W (ρ = 0.865, p < 0.0001), whereas significant correlation was found but was relatively weak between CSA5-10,R/W and MAAR/W (ρ = 0.512, p = 0.0003). The percentage of each lung zone to whole-lung CSA<5 had significant correlations with the percentage of each corresponding lung zone to whole-lung MAA. CONCLUSION. Pulmonary small vessels alteration, as measured by CSA on CT images, significantly correlated with pulmonary perfusion.