Mutations in the human PAH gene, which encodes phenylalanine hydroxylase are associated with varying degrees of hyperphenylalaninemia (HPA). The more severe of these manifest as a classic metabolic disease—phenylketonuria (PKU). In vitro expression analysis of PAHmutations has three major applications: 1) to confirm that a disease-associated mutation is genuinely pathogenic, 2) to assess the severity of a mutation's impact, and 3) to examine how a mutation exerts its deleterious effects on the PAH enzyme, that is, to elucidate the molecular mechanisms involved. Data on expression analysis of 81 PAH mutations in multiple in vitro systems is summarized in tabular form online at www.pahdb.mcgill.ca. A review of these findings points in particular to a prevalent general mechanism that appears to play a major role in the pathogenicity of many PAH mutations. Amino acid substitutions promote misfolding of the PAH protein monomer and/or oppose the correct assembly of monomers into the native tetrameric enzyme. The resulting structural aberrations trigger cellular defenses, provoking accelerated degradation of the abnormal protein. The intracellular steady-state levels of the mutant PAH enzyme are therefore reduced, leading to an overall decrease in phenylalanine hydroxylation within cells and thus to hyperphenylalaninemia. There is considerable scope for modulation of the enzymic and metabolic phenotypes by modification of the cellular handling—folding, assembly, and degradation—of the mutant PAH protein. This has major implications, both for our understanding of genotype-phenotype correlations and for the development of novel therapeutic approaches. Hum Mutat 21:357–369, 2003. © 2003 Wiley-Liss, Inc.