Objective: To evaluate the influence of a standardised sampling protocol and process quality across the different IDEFICS (Identification and prevention of dietary- and lifestyle-induced health effects in children and infants) centres on the results of the biochemical measurements. Design: Baseline survey within the community-based intervention study. Subjects: A total of 16 224 children, aged 2-8 years, enrolled in the IDEFICS baseline survey in 8 European countries. Venous or capillary blood samples were collected from 12 430 children, urine samples from 13 890 children and saliva samples from 14 019 children. Methods: A set of quality indicators was recorded for the biological blood, urine and saliva samples collected during the IDEFICS study. Results of blood and urine measurements were analysed and stratified by selected quality indicators. Results: Concentrations of biological markers in blood and urine measured during the IDEFICS baseline survey are associated with several quality indicators assessed in this study. Between-country variations of these biomarkers are described. It was confirmed that fasting has a big influence on the concentration of certain biomarkers. Biomarkers in morning urine samples may be erroneous if the study subjects void during the night or if samples are not taken from the very first morning urine. Conclusions: The analysed data underline that a standardised sampling protocol is of major importance, especially in multicentre studies, but non-compliance is ever present in spite of well-defined standard operation procedures. Deviations from the protocol should therefore always be documented to avoid error pertaining to the concentration of biological markers.