Abstract Background Because of the belief that Nairobi is a low risk zone for malaria, little empirical data exists on malaria risk in the area. The aim of this study was to explore the risk of perceived malaria and some associated factors in Nairobi informal settlements using self-reported morbidity survey. Methods The survey was conducted from May to August 2004 on 7,288 individuals in two informal settlements of Nairobi. Participants were asked to report illnesses they experienced in the past 14 days. Logistic regression was used to estimate the odds of perceived-malaria. The model included variables such as site of residence, age, ethnicity and number of reported symptoms. Results Participants reported 165 illnesses among which malaria was the leading cause (28.1%). The risk of perceived-malaria was significantly higher in Viwandani compared to Korogocho (OR 1.61, 95%CI: 1.10–2.26). Participants in age group 25–39 years had significantly higher odds of perceived-malaria compared to those under-five years (OR 2.07, 95%CI: 1.43–2.98). The Kikuyu had reduced odds of perceived-malaria compared to other ethnic groups. Individuals with five and more symptoms had higher odds compared to those with no symptoms (OR 23.69, 95%CI: 12.98–43.23). Conclusion Malaria was the leading cause of illness as perceived by the residents in the two informal settlements. This was rational as the number of reported symptoms was highly associated with the risk of reporting the illness. These results highlight the need for a more comprehensive assessment of malaria epidemiology in Nairobi to be able to offer evidence-based guidance to policy on malaria in Kenya and particularly in Nairobi.