Background: Trauma-related disorders and personality disorders are prevalent in survivors of chronic childhood trauma and neglect. Both conditions have serious consequences for patients, their families, society and public health and a high risk of development of chronicity. However, information on the long term course trajectories is lacking and predictors of course outcome in survivors of chronic childhood traumatization are unknown. The first aim of the current study is to identify two-year course trajectories of pathology in patients with trauma-related disorders and personality disorders. The second aim is to examine predictors of the course, including demographics, clinical characteristics and comorbidities. Methods/design: The study is a naturalistic two-year follow-up of 150 patients consecutively admitted to the trauma treatment program and the personality disorder treatment program respectively at GGZ Friesland, a regular Dutch mental health care center. The only exclusion criterion is insufficient mastery of the Dutch language. Participants will be assessed after 2years of treatment through measures that have been completed at baseline, including structured clinical interviews to measure childhood histories of trauma and neglect, (symptoms of) trauma-related disorders and personality disorders, and psychological questionnaire measures (e.g., general psychopathology, depressive symptoms and personality features). In addition, participants will complete an evaluation questionnaire to assess medication prescribed and treatment (s) received outside GGZ Friesland between baseline and follow-up. Information about (psychological and pharmacological) treatment received at GGZ Friesland during the follow-up period will be collected from patient files. Discussion: This study provides insight in the two-year course of (comorbid) trauma-related disorders and personality disorders. Identifying predictors of the course of trauma-related and personality disorders will allow to differentiate clinical profiles and will offer indicators for treatment.