Background: Child maltreatment is recognized as a widespread problem with huge implications for mental health and quality of life. Studies have repeatedly shown that victims of child maltreatment report significantly more adverse life outcomes than non-victims. The main objective of the study is (1) to examine the mental health and quality of life of maltreated children over a 1.5 year period beginning shortly after a report has been filed with an Advies- en Meldpunt Kindermishandeling (AMK) (advice and reporting center on child abuse and neglect). Secondary objectives are: (2) to examine how relevant determinants influence the mental health and quality of life of maltreated children, and (3) to examine differences in mental health and quality of life outcomes when comparing families of Dutch origin with families originating from Morocco and Suriname. Methods/Design. A prospective study will be performed, in which parent-child dyads will be followed over a 1.5 year period. Participants will be recruited shortly after the report to the AMK and they will be asked to complete a questionnaire four times, at baseline and every six months thereafter. Data will be analyzed using a longitudinal multi-level analysis. Discussion. The study is expected to yield evidence about the mental health and quality of life of maltreated children and about determinants that influence their mental health and quality of life outcomes. Strengths of this study are (1) the design which makes it possible to start examining outcomes shortly after or even during the actual maltreatment and to follow parent-child dyads for 1.5 years, and (2) asking children as informants about their own situation by making use of self-report questionnaires as much as possible. Limitations include the risks of selection bias and loss to follow-up during 1.5 years of data collection. Trial registration. NTR3674, funded by ZonMw, project 15700.2012. © 2013 Snoeren et al.; licensee BioMed Central Ltd.