Developing countries face a huge burden of infectious diseases, a number of which co-exist. This paper estimates the pattern and variation of malaria and diarrhea coexistence in Chikhwawa, a district in Southern Malawi using bivariate multilevel modelling with Bayesian estimation. A probit link was employed to examine hierarchically built data from a survey of individuals (n = 6,727) nested within households (n = 1,380) nested within communities (n = 33). Results show significant malaria [ ] and diarrhea [ ] variations with a strong correlation between them [ ] at household level. There are significant malaria [ ] and diarrhea [ ] variations at community level but with a small correlation [ ] between them. There is also significant correlation between malaria and diarrhea at individual level [ 0.241]. These results suggest a close association between reported malaria-like illness and diarrheal illness especially at household and individual levels in Southern Malawi.