Malaria is often a major health problem in countries undergoing war or conflict owing to breakdown of health systems, displacement of vulnerable populations, and the increased risk of epidemics. After 23 years of conflict, malaria has become prevalent in many rural areas of Afghanistan. From 1993 to the present, a network of non-governmental organizations, co-ordinated by HealthNet International, has operated a programme of bednet sales and re-treatment in lowland areas. To examine whether a strategy based on insecticide-treated nets (ITN) is a viable public health solution to malaria, communities were given the opportunity to buy nets and then monitored to determine population coverage and disease control impact. This was carried out using two contrasting methods: cross-sectional surveys and passive surveillance from clinics using a case-control design. Nets were purchased by 59% of families. Cross-sectional surveys demonstrated a 59% reduction in the risk of Plasmodium falciparum infection among ITN users compared with non-users (OR 0.41; 95% CI 0.25-0.66). The passive surveillance method showed a comparable reduction in the risk of symptomatic P. falciparum malaria among ITN users (OR 0.31; 95% CI 0.21-0.47). The cross-sectional method showed a 50% reduction in risk of P. vivax infection in ITN users compared with non-users (OR 0.50; 95% CI 0.17-1.49) but this effect was not statistically significant. The passive surveillance method showed a 25% reduction in the risk of symptomatic P. vivax malaria (OR 0.75; 95% CI 0.66-0.85). ITN appeared to be less effective against P. vivax because of relapsing infections; hence an effect took more than one season to become apparent. Passive surveillance was cheaper to perform and gave results consistent with cross-sectional surveys. Untreated nets provided some protection. Data on socioeconomic status, a potential confounding factor, was not collected. However, at the time of net sales, there was no difference in malaria prevalence between buyers and non-buyers. The abundance of Anopheles stephensi, the main vector, did not appear to be affected by ITN. ITN constitute one of the few feasible options for protection against malaria in chronic emergencies.