The objective of this study was to investigate the 4-week repeatability of contrast-agent based pulmonary perfusion quantification in clinically stable patients with COPD and CF. Software including fully automated lung segmentation was used to determine pulmonary blood flow (PBF). While a good agreement of PBF was found in the majority of patients, high variabilities were found. Several influence factors were considered as explanations. Differences in SNR due to different inspiratory levels are likely to influence whether quantification in each voxel succeeds. Thus, it may be necessary to modify voxel-based quantification to compensate for differences in inspiratory levels and low SNR.