Brain functional imaging methods, such as fMRI, are sensitive to changes in cerebral blood flow (CBF) that are normally associated with changes in regional neural activation. However, other endogenous and exogenous factors can alter CBF independently of brain neural activity, thus complicating the interpretation of functional imaging data. The presence of an anxiety disorder, as well as change in state anxiety, is often accompanied by respiratory alterations that affect arterial CO(2) tensions and produce significant changes in CBF that are independent of task-related neural activation. Therefore, the effects of trait and state anxiety need to be given close consideration in interpreting functional imaging findings. In this paper, we review the dependence of most brain functional imaging methods on localized changes in CBF and the potentially confounding effects of anxiety-related alterations of respiration on interpreting patterns of functional activation. Approaches for addressing these effects are discussed.