Children with fever are a majority in the various emergency rooms all over the world, and especially in the tropics. Most in sub-Saharan Africa will be treated for malaria, whether confirmed or not. It therefore follows that some of the morbidities other than malaria may go undiagnosed. The comorbidities with malaria that may have similar presentation among under-fives therefore are difficult to detect, and diseases like respiratory tract infections and urinary tract infections (UTI) are left to debilitate affected children. The exact burden of UTI co-existing with malaria in Nigeria remains ill defined. This study looks at the co-existence of UTI in under- fives with a primary diagnosis of malaria. Well-nourished children aged less than five years with confirmed malaria seen at the Children Emergency Room of the University of Benin Teaching Hospital were recruited into a prospective cross-sectional study between June and August 2006. The prevalence of UTI was 9% (27 of 300 children), with those aged less than 24 months comprising the majority. The uropathogens isolated included Staphylococcus aureus (55.6%), Escherichia coli (29.6%) and Kleibsiella pneumonia (14.8%). The isolates demonstrated high in vitro sensitivity to clavulanic acid-potentiated amoxicillin, ciprofloxacin and gentamicin, but were resistant to other commonly used antibiotics like amoxicillin and co-trimoxazole. The study indicates that UTI is a silent comorbidity in children aged less than 5 years with malaria and there is a need to evaluate these children in order to prevent the long-term morbidity of chronic renal diseases.