Background: Malaria and human immunodeficiency virus (HIV) are two major infections with enormous public health consequence. Together, they are endemic in many developing countries with anaemia being the most frequent haematological consequence of the infections. Objective: To determine the prevalence of malaria and HIV co-infection as well as anaemia among selected patients from three health-care institutions in Lagos, Nigeria. Methods: A cross-sectional study of 1080 patients was carried out to determine the prevalence of malaria and HIV coinfection as well as anaemia. Blood sera from each of the patients were screened for malaria parasites, HIV-1 and HIV-2 using Giemsa stain, Cambridge Biotech Recombigen HIV-1/HIV-2 rapid device, respectively while haemoglobin estimation was performed using cyanmethemoglobin method. Results: Our data showed that the total number of malaria infected patients were significantly higher in HIV sero-positive patients 47.7% (31/65) when compared with their HIV sero-negative counterparts 25.8% (262/1015) P = 0.047. The result also revealed that 25.8% (8/31) of the patients co-infected with malaria and HIV had anaemia as compared to 11.1% (29/ 262) infected with malaria alone. Multivariable logistic regression analysis showed that patients with dual infection of malaria and HIV were twice likely to be anaemic than those infected with malaria alone [adjusted OR 2.4, 95% CI, 1.3 to 2.7, P = 0.014]. Conclusion: Our data indicated a higher prevalence of malaria in HIV infected patients and also revealed that patients coinfected with malaria and HIV were more likely to be anaemic.