BACKGROUND: Evidence for a benefit of interventions to help women who screen positive for intimate partner violence (IPV) in health-care settings is limited. We assessed whether brief counselling from family doctors trained to respond to women identified through IPV screening would increase women's quality of life, safety planning and behaviour, and mental health. METHODS: In this cluster randomised controlled trial, we enrolled family doctors from clinics in Victoria, Australia, and their female patients (aged 16-50 years) who screened positive for fear of a partner in past 12 months in a health and lifestyle survey. The study intervention consisted of the following: training of doctors, notification to doctors of women screening positive for fear of a partner, and invitation to women for one-to-six sessions of counselling for relationship and emotional issues. We used a computer-generated randomisation sequence to allocate doctors to control (standard care) or intervention, stratified by location of each doctor's practice (urban vs rural), with random permuted block sizes of two and four within each stratum. Data were collected by postal survey at baseline and at 6 months and 12 months post-invitation (2008-11). Researchers were masked to treatment allocation, but women and doctors enrolled into the trial were not. Primary outcomes were quality of life (WHO Quality of Life-BREF), safety planning and behaviour, mental health (SF-12) at 12 months. Secondary outcomes included depression and anxiety (Hospital Anxiety and Depression Scale; cut-off ≥8); women's report of an inquiry from their doctor about the safety of them and their children; and comfort to discuss fear with their doctor (five-point Likert scale). Analyses were by intention to treat, accounting for missing data, and estimates reported were adjusted for doctor location and outcome scores at baseline. This trial is registered with the Australian New Zealand Clinical Trial Registry, number ACTRN12608000032358. FINDINGS: We randomly allocated 52 doctors (and 272 women who were eligible for inclusion and returned their baseline survey) to either intervention (25 doctors, 137 women) or control (27 doctors, 135 women). 96 (70%) of 137 women in the intervention group (seeing 23 doctors) and 100 (74%) of 135 women in the control group (seeing 26 doctors) completed 12 month follow-up. We detected no difference in quality of life, safety planning and behaviour, or mental health SF-12 at 12 months. For secondary outcomes, we detected no between-group difference in anxiety at 12 months or comfort to discuss fear at 6 months, but depressiveness caseness at 12 months was improved in the intervention group compared with the control group (odds ratio 0·3, 0·1-0·7; p=0·005), as was doctor enquiry at 6 months about women's safety (5·1, 1·9-14·0; p=0·002) and children's safety (5·5, 1·6-19·0; p=0·008). We recorded no adverse events. INTERPRETATION: Our findings can inform further research on brief counselling for women disclosing intimate partner violence in primary care settings, but do not lend support to the use of postal screening in the identification of those patients. However, we suggest that family doctors should be trained to ask about the safety of women and children, and to provide supportive counselling for women experiencing abuse, because our findings suggest that, although we detected no improvement in quality of life, counselling can reduce depressive symptoms. FUNDING: Australian National Health and Medical Research Council.