Objective To quantify and characterise missed opportunities for earlier HIV diagnosis in patients diagnosed with advanced HIV. Design A retrospective observational cohort study. Setting A central tertiary medical centre in Israel. Measures The proportion of patients with advanced HIV, the proportion of missed opportunities to diagnose them earlier, and the rate of clinical indicator diseases (CIDs) in those patients. Results Between 2010 and 2015, 356 patients were diagnosed with HIV, 118 (33.4%) were diagnosed late, 57 (16%) with advanced HIV disease. Old age (OR=1.45 (95% CI 1.16 to 1.74)) and being heterosexual (OR=2.65 (95% CI 1.21 to 5.78)) were significant risk factors for being diagnosed late. All patients with advanced disease had at least one CID that did not lead to an HIV test in the 5 years prior to AIDS diagnosis. The median time between CID and AIDS diagnosis was 24 months (IQR 10–30). 60% of CIDs were missed by a general practitioner and 40% by a specialist. Conclusions Missed opportunities to early diagnosis of HIV occur in primary and secondary care. Lack of national guidelines, lack of knowledge regarding CIDs and communication barriers with patients may contribute to a late diagnosis of HIV.