OBJECTIVE: Coordination of health interventions and research is often weak during periods of political transition and unprecedented aid inflows, which Cambodia has recently experienced. Although HIV, tuberculosis (TB), and malaria have been a focus of international funding, TB has received much less. This study compares the numbers and methodologies of studies conducted on TB, malaria, and HIV in Cambodia, identifying evidence gaps and future research needs. METHODS: Three electronic databases and the grey literature were searched for studies on HIV, TB, and malaria published between January 2000 and October 2015. Information about the disease focus and methodology was extracted from the studies included. RESULTS: A total of 2581 unique studies were screened and 712 were included in the analysis. The results of this review demonstrated that despite increasing numbers of publications, there have been fewer studies on TB (16%) than HIV (43%) and malaria (41%). Observational epidemiological studies outnumbered other methodologies (44%) for all three diseases. CONCLUSIONS: Despite substantial investments, important research areas appear to have been neglected in Cambodia; specifically, studies on TB and studies involving economic, qualitative, interventional, and genomics methods. The inter-disease disparity in published research in Cambodia identified, considered alongside disease burden, suggests that an increase in TB research may be needed to inform control strategies.