Recent research has described the structure of psychopathology as including one general and multiple specific factors, and this structure has been found in samples across development. However, little work has examined whether this structure is consistent across time, particularly in young children, within the same sample. Further, few studies have examined factors that influence the magnitude of the stability of latent dimensions of psychopathology. In the present study, we examine these issues in a community sample of 545 children assessed at ages 3 and 6. In addition, we explored child temperament, parental history of psychopathology, and parenting behaviors as potential moderators of the longitudinal stability of latent dimensions of psychopathology. We found that the same bifactor model structure identified at age 3 provided an adequate fit to the data at age 6. Further, our model revealed significant homotypic stability of the general, internalizing, and externalizing specific factors. We also found evidence of differentiation of psychopathology over time with the general factor at age 3 predicting the externalizing factor at age 6. However, we failed to identify moderators of the longitudinal associations between psychopathology latent factors. Overall, our results bolster support for the bifactor structure of psychopathology, particularly in early childhood.