We examined the usefulness of measuring cytomegalovirus (CMV) viral load (VL) in blood using quantitative polymerase chain reaction (qPCR) in establishing a diagnosis of CMV end-organ disease in consecutive unwell HIV-infected patients. The indication for testing for CMV, CD4 count, CMV VL and presence of CMV end-organ disease were abstracted from case-notes. During a 42-month period, 216 tests were performed in 181 patients; the majority (61%) had CD4 counts < 100 cells/μL. The prevalence of detectable CMV by qPCR was 43.5% (94/216) with a prevalence of CMV end-organ disease of 7.4% (16/216). Of patients with CMV detectable by qPCR, 72 % (50/69) had CD4 counts < 100 cells/μL. For patients with definite CMV end-organ disease, the positive predictive value of detectable CMV by qPCR was 10% (9/94), and the negative predictive value was 98% (119/122). In acutely unwell HIV-infected patients, detection of CMV by qPCR is a poor predictor of CMV end-organ disease.