BACKGROUND: Malaria is a leading cause of death in children below five years of age in sub-Saharan Africa. All-cause and malaria-specific mortality rates for children under-five years old in a mesoendemic malaria area (The Gambia) were compared with those from a hyper/holoendemic area (Burkina Faso). METHODS: Information on observed person-years (PY), deaths and cause of death was extracted from online search, using key words: "Africa, The Gambia, Burkina Faso, malaria, Plasmodium falciparum, mortality, child survival, morbidity". Missing person-years were estimated and all-cause and malaria-specific mortality were calculated as rates per 1,000 PY. Studies were classified as longitudinal/clinical studies or surveys/censuses. Linear regression was used to investigate mortality trends. RESULTS: Overall, 39 and 18 longitudinal/clinical studies plus 10 and 15 surveys and censuses were identified for The Gambia and Burkina Faso respectively (1960-2004). Model-based estimates for under-five all-cause mortality rates show a decline from 1960 to 2000 in both countries (Burkina Faso: from 71.8 to 39.0), but more markedly in The Gambia (from 104.5 to 28.4). The weighted-average malaria-specific mortality rate per 1000 person-years for Burkina Faso (15.4, 95% CI: 13.0-18.3) was higher than that in The Gambia (9.5, 95% CI: 9.1-10.1). Malaria mortality rates did not decline over time in either country. CONCLUSION: Child mortality in both countries declined significantly in the period 1960 to 2004, possibly due to socio-economic development, improved health services and specific intervention projects. However, there was little decline in malaria mortality suggesting that there had been no major impact of malaria control programmes during this period. The difference in malaria mortality rates across countries points to significant differences in national disease control policies and/or disease transmission patterns.