Objective: Human Immunodeficiency Viral infection and Protein Energy Malnutrition (PEM) are highly prevalent in Nigeria and when they occur together, the outcome is usually severe as both conditions lead to immune suppression. HIV alone accounts for 14.0% of childhood mortality even though children constitute only 6% of global HIV infection burden. The objective of the study was to determine the prevalence of HIV infection among malnourished children below 5 years in Kano State, Nigeria. Methods: A total of 400 malnourished children were randomly selected and tested for the presence of HIV I & II using parallel ELISA rapid test kits, Stat park and Determine (both immunochromatographic techniques). Findings: Thirty-one samples were found to be positive to HIV 1 giving a prevalence of 7.8%. There was no statistically significant difference between sexes when male to female ratio was 1:1.3 and peak age of presentation was 2 -3 years. Sixty-four percent (64.0%) were presented with severe form of HIV infection (stage 4) according to WHO paediatric HIV clinical stage and about half of them came with marasmus by the Wellcome classification of malnutrition. There was no significant association between the type of malnutrition and the severity of HIV infection at present, (p value > 0.05). The commonest signs and symptoms were oral candidiasis (67.7%), lymphadenopathy (44.0%), fever (64.5%) and cough (54.8%). Sixty-four percent of the children were from polygamous families. There was a significant statistical correlation between polygamy and incidence of HIV infection, (p < 0.01). Only 45.0% of the women were aware of their HIV status prior to this study. Seventy-four percent (74.0%) of those who were aware of their status had no knowledge of the prevention of mother to child transmission (PMTCT) services and even for those who were aware, none of them accessed the care. Conclusion: A population based HIV screening is therefore recommended while perinatal HIV screening and PMTCT services need to be expanded.