What can psychopathology and its treatment tell us about cognitive emotional interactions? Standard approaches to interactions between emotion and cognition often adopt a variant of the idea that cognitive processes, subserved by dorsal and lateral cortical circuits, exert control and regulation of ventral, limbic brain areas associated with emotional expression and experience. However, it is becoming clear from studies on depression, post-traumatic stress disorder (PTSD) and obsessive compulsive disorder (OCD), that a binary, opponent theory of cognitive emotion interaction (CEI) and the dorsal-ventral model of neurocircuitry do not fully describe the data. We summarize recent research to suggest that networks of direct and indirect pathways exist by which cognition can regulate pathological emotion, and the inter-relationships of specific nodes within the networks need to be characterized.