Background: Children who witness interparental violence are at a heightened risk for developing psychosocial, behavioral and cognitive problems, as well as posttraumatic stress symptoms. For these children the psycho-educational secondary prevention program 'En nu ik...!' ('It's my turn now!') has been developed. This program includes specific therapeutic factors focused on emotion awareness and expression, increasing feelings of emotional security, teaching specific coping strategies, developing a trauma narrative, improving parent-child interaction and psycho-education. The main study aim is to evaluate the effectiveness of the specific therapeutic factors in the program. A secondary objective is to study mediating and moderating factors.Methods/design: This study is a prospective multicenter randomized controlled trial across cities in the Netherlands. Participants (N = 140) are referred to the secondary preventive intervention program by police, social work, women shelters and youth (mental health) care. Children, aged 6-12 years, and their parents, who experienced interparental violence are randomly assigned to either the intervention program or the control program. The control program is comparable on nonspecific factors by offering positive attention, positive expectations, recreation, distraction, warmth and empathy of the therapist, and social support among group participants, in ways that are similar to the intervention program. Primary outcome measures are posttraumatic stress symptoms and emotional and behavioral problems of the child. Mediators tested are the ability to differentiate and express emotions, emotional security, coping strategies, feelings of guilt and parent-child interaction. Mental health of the parent, parenting stress, disturbances in parent-child attachment, duration and severity of the domestic violence and demographics are examined for their moderating effect. Data are collected one week before the program starts (T1), and one week (T2) and six months (T3) after finishing the program. Both intention-to-treat and completer analyses will be done.Discussion: Adverse outcomes after witnessing interparental violence are highly diverse and may be explained by multiple risk factors. An important question for prevention programs is therefore to what extent a specific focus on potential psychotrauma is useful. This trial may point to several directions for optimizing public health response to children's exposure to interparental violence.Trial registration: Netherlands Trial Register (NTR): NTR3064. © 2012 Overbeek et al; licensee BioMed Central Ltd.