BACKGROUND: Implementation of known effective interventions would necessitate the reduction of malaria burden by half by the year 2010. Identifying geographical disparities of coverage of these interventions at small area level is useful to inform where greatest scaling-up efforts should be concentrated. They also provide baseline data against which future scaling-up of interventions can be compared. However, population data are not always available at local level. This study applied spatial smoothing methods to generate maps at subdistrict level in Malawi to serve such purposes. METHODS: Data for the following responses from the 2000 Malawi Demographic and Health Survey (DHS) were aggregated at subdistrict level: (1) households possessing at least one bednet; (2) children under 5 years who slept under a bednet the night before the survey; (3) bednets retreated with insecticide within past 6-12 months preceding the survey; (4) children under 5 who had fever two weeks before the survey and received treatment within 24 hours from the onset of fever; and (5) women who received intermittent preventive treatment of malaria during their last pregnancy. Each response was geographically smoothed at subdistrict level by applying conditional autoregressive models using Markov Chain Monte Carlo simulation techniques. RESULTS: The underlying geographical patterns of coverage of indicators were more clear in the smoothed maps than in the original unsmoothed maps, with relatively high coverage in urban areas than in rural areas for all indicators. The percentage of households possessing at least one bednet was 19% (95% credible interval (CI): 16-21%), with 9% (95% CI: 7-11%) of children sleeping under a net, while 18% (95% CI: 16-19%) of households had retreated their nets within past 12 months prior to the survey. The northern region and lakeshore areas had high bednet coverage, but low usage and re-treatment rates. Coverage rate of children who received antimalarial treatment within 24 hours after onset of fever was consistently low for most parts of the country, with mean coverage of 4.8% (95% CI: 4.5-5.0%). About 48% (95% CI: 47-50%) of women received antimalarial prophylaxis during their pregnancy, with highest rates in the southern and northern areas. CONCLUSION: The striking geographical patterns, for example between predominantly urban and rural areas, may reflect spatial differences in provider compliance or coverage, and can partly be explained by socio-economic and cultural differences. The wide gap between high bed net coverage and low retreatment rates may reflect variation in perceptions about malaria, which may be addressed by implementing information, education and communication campaigns or introducing long lasting insecticide nets. Our results demonstrate that DHS data, with appropriate methodology, can provide acceptable estimates at sub-national level for monitoring and evaluation of malaria control goals.