We examined longitudinal associations of resting heart rate (RHR) and general intelligence (IQ) with two psychopathology models (correlated factors and general factor model). RHR and IQ were measured during conscription (mean age = 18.23 years; N = 899,398 Swedish males). A correlated factors model of register-based outcomes (including 10 psychiatric diagnoses, criminal convictions, and prescription of anxiolytic medications; mean age at follow-up = 43.09 years) identified internalizing, externalizing, and psychotic dimensions; the general factor model additionally identified a general dimension. All correlated factors were inversely associated with IQ; however, the general factor model showed that several of these associations were attributable to general variance rather than specific variance. In both psychopathology models, RHR weakly but significantly predicted higher internalizing but lower externalizing problems. Intelligence might be a transdiagnostic risk factor for any form of psychopathology, and the internalizing and externalizing spectra might be differentiated by psychobiological processes related to sensitivity to punishment.