In many British hospitals, HIV-positive patients access care via genitourinary (GU) medicine services. As a result of National Health Service (NHS) legislation, such patients may have information concerning HIV treatment filed separately from their general clinical records. We sought to evaluate accuracy of medication records of patients with both GU medicine and general hospital case-notes, and to assess clinical risk arising from incorrect or incomplete recording. In this retrospective review, 156 episodes of care from 100 HIV-positive patients with separate HIV case-notes were evaluated for accuracy of medication recording, when paired with clinical notes from attendances in other hospital departments. Discrepancies were observed in 52.6% of care episodes; significant discrepancies were apparent in 7.8%. The dual case-note system represents significant risk to patient care. We recommend that hospitals that continue to operate this system urgently consider amalgamation of HIV care records into hospital case sheets, in line with current national standards.