Cerebrovascular reactivity can be measured using blood oxygen level dependent (BOLD) MRI and is a potential mechanism in cerebral small vessel disease (SVD). Investigations of the effect of field strength on CVR have been limited, particularly in patient groups. In this study CVR measurements within a series of preselected regions in SVD patients were assessed at 1.5 and 3T. Mean CVR was greater at 3T in 12 of the 14 regions, however differences, as assessed with Bland-Altman plots, were within reasonable limits. These results point to the importance of considering other scanner specific factors beyond field strength when measuring CVR.