Ten different indices of dietary control (IDCs) applied frequently to investigate compliance of phenylketonuric patients were calculated for a set of blood phenylalanine levels for 98 patients in the German Collaborative Study of Children Treated for Phenylketonuria during their first 9 years of life. The results were compared for similarities and differences. Cluster analysis of longitudinal phenylalanine data was introduced to analyse phenylalanine blood levels independent of a priori defined criteria of classification. Three groups of good, intermediate and poor long-term dietary control were identified. Internal validation of the IDCs was corroborated by the high inter-correlations of the indices. External validity was determined by the inter-relations of the WISC-R IQ and the IDCs. The different algorithms of IDCs suggest different clinical conclusions. To facilitate comparisons of results of future research, IDCs should be standardized.