Objective: To explore the relationship between temperament and character traits in Cloninger’s psychobiological theory and mental disorders. Methods: A systematic literature search was conducted of five international databases for all articles published in English between January 1990 and April 2019 (PROSPERO-CRD42019133214). Owing to heterogeneity, pooled estimates of correlations for personality disorders and standardized mean differences for case–control studies related to other mental disorders were calculated using the random-effects method. Results: The pooled effect sizes obtained from 149 studies showed that high harm avoidance (related to 22/24 diagnostic categories), low self-directedness (21/23), low cooperativeness (17/23), high self-transcendence (14/23), low reward dependence (11/24), high novelty-seeking (10/24), low novelty-seeking (7/24), high persistence (2/23), low persistence (2/23) and high reward dependence (2/24) were related to psychopathology. Conclusions: All traits provided unique psychobiological tools for differential diagnosis of mental disorders. However, high harm avoidance and low self-directedness played a canonical role in psychopathology. Despite the study limitations, additional studies are warranted to evaluate the differential diagnoses suggested by the present model.