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Abstract Background Insecticide-treated bed nets (ITNs) are known to be highly effective in reducing malaria morbidity and mortality. The effectiveness of ITNs is largely influenced by behavioural factors and not much is known regarding such factors under programme conditions. Methods This descriptive study was nested into a large ITN effectiveness study in rural Burkina Faso. During two cross-sectional surveys in the dry and rainy season of 2003, random samples of young children from nine representative villages (n = 180 per survey) were investigated for compliance with ITN protection and related behaviour. Data were collected through direct observations and through interviews with mothers. Results ITNs were perceived as very important for protection against mosquitoes and malaria particularly during the rainy season, but there were problems with their use during the dry season. Young children usually slept with their mother under the ITN and self-reported compliance was 66% and 98% during dry and rainy season, respectively (confirmed by direct observation in 34% and 79%, respectively). Important reasons for low compliance during the dry season were high temperatures inside houses and problems related to changing sleeping places during the night. Conclusion Under programme conditions, compliance with ITN protection in young children is sufficient during the rainy season, but is rather low during the hot and dry season. Greater emphasis needs to be placed on information/education efforts to make people aware of the fact that the risk of contracting malaria may persist throughout the year.