Prospective studies investigating the long-term stability of depression symptom subtypes are rare. Moreover, sex has received little attention as a predictor. This study aimed to investigate the role of sex on stability and transition patterns of depressive symptom subtypes over 20 years. The data were drawn from three follow-ups (1988, 1999, and 2008) of the longitudinal Zurich Study. Latent transition analyses were fitted to the data of 322 subjects, using depressive symptoms from the face-to-face interviews. The stable classes were characterized by psychosocial correlates. Three subtypes were identified: 'severe atypical,' 'severe typical,' and 'moderate.' While stability of the severe atypical and moderate subtype was relatively high and increased over time (70-71; 45-90 %), stability of the severe typical subtype was lower (45-48 %). Females had a higher risk of being in the severe atypical subtype and exhibited more transitions, particularly with respect to the severe typical subtype. In contrast, males displayed more stable subtypes. The stable severe atypical subtype was associated with comorbid eating disorders as well as psychosis syndromes, whereas the stable severe typical subtype was associated only with psychosis syndromes. Our results provide first evidence for the notion that long-term stability and transition patterns differ by sex and depression subtypes. This finding has received too little attention in previous research and should be considered in treatments.