Integrative hierarchical models have sought to account for the extensive comorbidity between various internalizing disorders in terms of broad individual difference factors these disorders share. However, such models have been developed largely on the basis of self-report and diagnostic symptom data. Toward the goal of linking such models to neurobiological systems, we reviewed studies that have employed variants of the affect-modulated startle paradigm to investigate emotional processing in internalizing disorders as well as personality constructs known to be associated with these disorders. Specifically, we focused on four parameters of startle reactivity: fear-potentiated startle, inhibition of startle in the context of pleasant stimuli, context-potentiated startle, and general startle reactivity. On the basis of available data, we argue that these varying effects index differing neurobiological processes related to mood and anxiety disorders that are interpretable from the standpoint of dimensional models of the internalizing spectrum. Further, we contend that these empirical findings can feed back into and help reshape conceptualizations of internalizing disorders in ways that make them more amenable to neurobiological analysis.