Although heterogeneity of depression hinders research and clinical practice, attempts to reduce it with latent variable models have yielded inconsistent results, probably because these techniques cannot account for all interacting sources of heterogeneity at the same time. Therefore, to simultaneously decompose depression heterogeneity on the person-, symptom and time-level, three-mode Principal Component Analysis (3MPCA) was applied to data of 219 Major Depression patients, who provided Beck Depression Inventory assessments every three months for two years. The resulting person-level components were correlated with external baseline clinical and demographic variables. The 3MPCA extracted two symptom-level components ('cognitive', 'somatic-affective'), two time-level components ('improving', 'persisting') and three person-level components, characterized by different interaction-patterns between the symptom-and time-components ('severe non-persisting', 'somatic depression' and 'cognitive depression'). This model explained 28% of the total variance and 65% when also incorporating the general trend in the data). Correlations with external variables illustrated the content differentiation between the person-components. Severe non-persisting depression was positively correlated with psychopathology (r=0.60) and negatively with quality of life (r=-0.50). Somatic depression was negatively correlated with physical functioning (r=-0.45). Cognitive depression was positively correlated with neuroticism (r=0.38) and negatively with self-esteem (r=-0.47). In conclusion, 3MPCA decomposes depression into homogeneous entities, while accounting for the interactions between different sources of heterogeneity, which shows the utility of the technique to investigate the underlying structure of complex psychopathology data and could help future development of better empirical depression subtypes.