A. Fuglsang [Biochem. Biophys. Res. Commun. 317 (2004) 957-964] suggested that effective number of codons for individual amino acids (AY-values) should be re-adjusted to the number of synonymous codons of those amino acids, in order to prevent the overestimation of the effective number of codons. Here, it is shown that re-adjustment at the level of individual amino acids results in loss of considerable amounts of information. Furthermore, we have shown that theoretical N-c-values arc functions of GC3s (and GC1s); as a result, when an amino acid N-c-value exceeds the related theoretical Nc-value, the implication of re-adjustment depends on the GC composition of the gene. (C) 2004 Elsevier Inc. All rights reserved.