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Since 1992, German soldiers have been deployed in areas where malaria is endemic. Antimalarial chemoprophylaxis (CP) is directed according to the assessed risk and is provided free of charge. Compliance is crucial if its effect is to be reliable. This study analysed compliance with directed CP in German soldiers as well as its determinants.Between 2003 and 2009, standardized questionnaire-based interviews were performed with 2,149 out of approximately 100,000 German soldiers who were deployed during this period in areas where malaria is endemic. The questionnaires dealt with information that the soldiers had received about malaria prior to their missions, with their adherence to mosquito-protective and antimalarial chemoprophylactic procedures, and their estimations of their individual level of exposure.About 1,308 out of 2,149 interviewed soldiers had been ordered to take CP, allowing for an assessment of the outcome parameter "CP-compliance". About 76.9 % out of 1,308 soldiers to whom regular CP was directed took it regularly. The exposure variables "age", "satisfaction with malaria counselling", "perceived threat due to insects or mosquitoes" and "use of insect repellents" were positively associated with compliance with directed antimalarial CP.The study confirms the findings of the French and US armies that even free-of-charge access to antimalarial medication will not lead to 100 % acceptance. The compliance problem is aggravated by the generally low age of deployed soldiers. Adequate counselling is crucial to increase adherence to antimalarial CP.