Children in less developed countries die from relatively small number of infectious disease, some of which epidemiologically overlap. Using self-reported illness data from the 2000 Malawi Demographic and Health Survey, we applied a random effects multinomial model to assess risk factors of childhood co-morbidity of fever, diarrhoea and pneumonia, and quantify area-specific spatial effects. The spatial structure was modelled using the conditional autoregressive prior. Various models were fitted and compared using deviance information criterion. Inference was Bayesian and was based on Markov Chain Monte Carlo simulation techniques. We found spatial variation in childhood co-morbidity and determinants of each outcome category differed. Specifically, risk factors associated with child co-morbidity included age of the child, place of residence, undernutrition, bednet use and Vitamin A. Higher residual risk levels were identified in the central and southern–eastern regions, particularly for fever, diarrhoea and pneumonia; fever and pneumonia; and fever and diarrhoea combinations. This linkage between childhood health and geographical location warrants further research to assess local causes of these clusters. More generally, although each disease has its own mechanism, overlapping risk factors suggest that integrated disease control approach may be cost-effective and should be employed.