To quantify lung parenchymal changes in symptomatic patients with chronic pulmonary graft-versus-host disease 3 years after allogeneic stem cell transplantation (allo-SCT) by means of CT-densitometry (CTD) and to compare results with those of established pulmonary function tests (PFT). The study group consisted of 26 patients with pulmonary cGvHD (19 males, 7 females; mean age, 49.29±15.89; range, 19-72 years). The diagnosis was based on clinical symptoms, PFT and chest-CT findings. CTD and PFT were performed both in the pre- and post-transplantation setting and results compared with each other. CT scans were obtained during suspended deep inspiration including the whole lungs. The mean lung attenuation (MLD), low attenuation values (LAV) and distribution of focal parenchymal abnormalities compatible with emphysema (HU <-950) were quantitatively calculated with histograms and graphics. On PFT, total lung capacity (TLC), residual volume (RV), vital capacity (VC), forced expiratory volume in 1 s (FEV1s) and diffusion capacity for carbon monoxide (DLCOSB) were registered. Changes in end-inspiratory lung volume and density (MLD and LAV) in symptomatic cGvHD patients in mean three years after allo-SCT proved all not significant, but there was a clear trend towards an increase in lung volume and a decrease in lung attenuation. These results were similar throughout all classes of bronchiolitis obliterans (BO) by cGvHD. PFT showed a significant decrease in VC, FEV1s but only a minimal decrease in DLCOSB. Changes in FVC after stem cell transplantation correlated with changes in LAV (r=0.649, P=0.031). Predicted VC correlated with changes in LAV (r=0.771, P=0.005). There was a correlation between the absolute difference of FEV1 and DLCOSB (r=0.64, P=0.14) before and after stem cell transplantation. End-inspiratory phase CT lung parenchyma quantification in symptomatic patients with pulmonary cGvHD 3 years after allo-SCT shows discrete changes over the pre-transplantation setting representing airway obstruction, mirroring airflow limitation on PFT. Its use enables exclusion of relevant parenchymal destruction (emphysema-equivalent lung density) at this time.