Background: There is substantial comorbidity between trauma-related disorders (TRDs), dissociative disorders (DDs) and personality disorders (PDs), especially in patients who report childhood trauma and emotional neglect. However, little is known about the course of these comorbid disorders, despite the fact that this could be of great clinical importance in guiding treatment. Objective: This study describes the two-year course of a cohort of patients with (comorbid) TRDs, DDs and PDs and aims to identify possible predictors of course. Possible gender differences will be described, as well as features of non-respondents. Method: Patients (N = 150) referred to either a trauma treatment program or a PD treatment program were assessed using five structured clinical interviews for diagnosing TRDs, DDs, PDs and trauma histories. Three self-report questionnaires were used to assess general psychopathology, dissociative symptoms and personality pathology in a more dimensional way. Data on demographics and received treatment were obtained using psychiatric records. We described the cohort after a two-year follow-up and used t-tests or chi-square to test possible differences between respondents and non-respondents and between women and men. We used regression analysis to identify possible course predictors. Results: A total of 85 (56.7%) of the original 150 patients participated in the follow-up measurement. Female respondents reported more sexual abuse than female non-respondents. Six patients (4.0%; all women) died because of suicide. Levels of psychopathology significantly declined during the follow-up period, but only among women. Gender was the only significant predictor of change. Conclusions: Comorbidity between TRDs, DDs and PDs was more the rule than the exception, pleading for a more dimensional and integrative view on pathology following childhood trauma and emotional neglect. Courses significantly differed between men and women, advocating more attention to gender in treatment and future research.