INTRODUCTION: Home-based HIV counselling & testing (HBHCT) is highly acceptable and has the potential to increase HIV testing uptake in sub-Saharan Africa. However, data are lacking on strategies that can effectively link HIV-positive individuals identified through HBHCT to care. This trial was designed to assess the effectiveness of two brief home-based counselling sessions on linkage to care, provided subsequent to referral for care among HIV-positive patients identified through HBHCT in a rural community in Masaka district, Uganda. METHODS: 28 communities (clusters) were randomly allocated to control (referral only) and intervention (referral and follow-up counselling) arms (n = 14 clusters/arm). Randomisation was stratified on distance from the district capital (≤10 km vs > 10 km) and cluster size (larger single village vs combined small villages), and restricted to ensure balance on selected cluster characteristics. A list of possible allocations was generated and one randomly selected at a public ceremony. HBHCT is being offered to all adults (≥18 years), and HIV-positive individuals not yet in care are eligible for enrolment. The intervention is provided at one and two months post-enrolment. Primary outcomes, assessed 6 months after enrolment, are: the proportion of individuals linking to HIV care within 6 months of HIV diagnosis and time to linkage. The primary analysis will be based on individual-level data. DISCUSSION: This study will provide evidence on the impact of a counselling intervention on linkage to care among adults identified with HIV infection through HBHCT. Interpretation of the trial outcomes will be aided by results from an on-going qualitative sub-study.