Large scale international multicentre studies require sophisticated quality management for the collection, processing and logistics of biological samples to ensure a maximum degree of standardisation across different environmental conditions and settings. This paper describes a quality management system for the collection of biological samples (QMS-BS) which was applied during IDEFICS, a large European multicentre study. The application was evaluated by several criteria like response rates for the different types of biological samples, measures of sample quality, compliance with the QMS-BS and efficiency of the document and sample control and of the quality assurance system. Response rates varied from 56.6% for venous blood collection to 90.1% for saliva collection. All sample types were associated with problems of sample quality (e.g. haemolysis of blood samples, lack of cooling for urine samples or desiccation of saliva samples). Overall compliance with the QMS-BS was good, with some exceptions mainly related to sample control. In conclusion the QMS-BS is a valuable tool for the management of biological sample collection in epidemiological multicentre studies.