A programme for proficiency testing of biochemical genetics laboratories undertaking urinary qualitative organic acid analysis and its results for 50 samples examined for factors contributing to poor performance are described. Urine samples from patients in whom inherited metabolic disorders have been confirmed as well as control urines were circulated to participants and the results from 94 laboratories were evaluated. Laboratories showed variability both in terms of their individual performance and on a disease-specific basis. In general, conditions including methylmalonic aciduria, propionic aciduria, isovaleric aciduria, mevalonic aciduria, Canavan disease and 3-methylcrotonyl-CoA carboxylase were readily identified. Detection was poorer for other diseases such as glutaric aciduria type II, glyceric aciduria and, in one sample, 3-methylcrotonyl-CoA carboxylase deficiency. To identify the factors that allow some laboratories to perform well on a consistent basis while others perform badly, we devised a questionnaire and compared the responses with the results for performance in the scheme. A trend towards better performance could be demonstrated for those laboratories that regularly use internal quality control (QC) samples in their sample preparation (p = 0.079) and those that participate in further external quality assurance (EQA) schemes (p = 0,040). Clinicians who depend upon these diagnostic services to identify patients with these defects and the laboratories that provide them should be aware of the potential for missed diagnoses and the factors that may lead to improved performance.