BACKGROUND: Malaria is associated with an increase in HIV viral load and a fall in CD4-cell count. Conversely, HIV infection disrupts the acquired immune responses to malaria and the efficacy of antimalarial drugs. This study was carried out in five Ghanaian hospitals to estimate the prevalence of clinically confirmed malaria among HIV patients by evaluating their hospital records. METHODS: This retrospective descriptive cross sectional study reviewed and collected data on malaria, using Case Record Forms from HIV patients' folders in five hospitals in Ghana. RESULTS: There were 933 patients records made up of 272 (29.2%) males and 661 (70.8%) females. Majority of the patients were aged between 21-40 (63.6%) years and the rest were between the ages 1-20 (2.8%) years, 41-60 (31.6%) years and 61-80 (2.1%) years of age.A total of 38.1% (355/933) of the patients were clinically suspected of having clinical malaria. Of these 339 (95.5%) were referred to the laboratory for confirmation of the diagnosis of malaria. Only 4.4% (15/339) of patients tested were confirmed as cases of malaria among the patients that were clinically suspected of having malaria and subsequently confirmed. Fever, was not significantly associated with a confirmed diagnosis of malaria [OR = 3.11, 95% CI: (0.63, 15.37), P = 0.142]. CONCLUSIONS: There was a 4.4% prevalence of confirmed malaria and 38.1% of presumptively diagnosed malaria from the case records of HIV patients from the selected hospitals in Ghana.