Type III hyperlipoproteinemia (HLP) is usually associated with homozygosity for apolipoprotein (apo) E2 (Arg112 --> Cys, Arg158 --> Cys). This common apo E isoform is defective in its binding to lipoprotein receptors. However, other rare mutations in the apo epsilon gene may also, in part dominantly, predispose to the disease. In order to assess the prevalence of rare apo E variants and mutations in the apo epsilon gene in Germany, we examined apo epsilon genotypes by restriction isotyping (RI) and apo E phenotypes by isoelectric focusing (IEF) in 107 German patients with type III HLP. Concordance between apo epsilon genotype and apo E phenotype was observed in 101 subjects (94.4%). Six individuals (5.6%) had genotypes and phenotypes other than E2/2. One subject was apparently homozygous for apo E2 by IEF, but heterozygous for epsilon3/2 by RI. Sequencing of the apo epsilon gene disclosed a hitherto undescribed point mutation (TGG --> TGA) at the third position of the codon for amino acid 20 (Trp), introducing a premature termination codon. This is the first study demonstrating that in the German population type III HLP is mainly associated with homozygosity for apo E2 (Arg112 --> Cys, Arg158 --> Cys) and that discrepancies between apo epsilon genotype and apo E phenotype are rare in this genetic condition.