BACKGROUND: Health facility data are more readily accessible for operational planning and evaluation of disease control programmes. The importance, potential challenges and limitations of using facility based survey as an alternative tool for monitoring changes in local malaria epidemiology were examined. METHODS: The study involved six areas within the administrative divisions of The Gambia. The areas were selected to reflect socioeconomic and malaria transmission intensities across the country. The study design involved an age stratified cross sectional surveys that were conducted during the wet season in 2008 and in the 2009 during the dry season. Participants were patients attending clinics in six health centres and the representative populations from the catchment communities of the health centres. RESULTS: Overall participants' characteristics were mostly not comparable in the two methodological approaches in the different seasons and settings. More females than males were enrolled (55.8 vs. 44.2 %) in all the surveys. Malaria infection was higher in the surveys in health centres than in the communities (p < 0.0001) and also in males than in females (OR = 1.3; p < 0.001). Males were less likely than females to sleep under an insecticide treated net in the communities (OR = 1.6; 95 % CI 1.3, 1.9) and in the health centres (OR = 1.3; 95 % CI 1.1, 1.5). Representativeness of the ethnic groups was better in the health centre surveys than in the community surveys when compared to the 2003 national population census in The Gambia. CONCLUSION: Health facility based survey though a potential tool for monitoring changes in the local epidemiology of malaria will require continuous validation of the facility and participants sociodemograhic characteristics as these may change over time. The effects of health seeking practices on service utilization and health facility surveys as an approach will also need continuous review.