Type III hyperlipoproteinemia (HLP III) is characterized by the reduced catabolism and accumulation of chylomicron and very low density lipoprotein (VLDL) remnants. Most HLP III patients are homozygous for the apolipoprotein E2 (Cys112, Cys158) allele; however, several other mutations at this gene locus have been associated with this HLP. In order to assess the presence of rare apo E variants in our population, we have examined apo E phenotypes by isoelectric focusing (IEF) and genotypes by restriction enzyme analysis of polymerase chain reaction (PCR) amplified DNA in 15 patients with HLP III. Lack of concordance between these two methods was observed in 11 subjects (73.3%). DNA sequencing analysis of the receptor binding domain of the apo E gene in the 11 HLP III patients with discrepancies demonstrated the presence of six carriers of the epsilon 3(Arg136-->Ser) allele and three carriers of the epsilon 2(Gly127-->Asp) allele. Five HLP III patients were apo E2/E2 using IEF, but only 2 of them were epsilon 2 homozygous using PCR. Two patients were E3/E3 homozygous with normal DNA sequence in the low density lipoprotein receptor binding domain of apo E. In conclusion, our results show that a number of different apo E genotypes are associated with HLP III in this population. More specifically, mutations at positions 127 and 136 might be frequent in Spain and occur in patients with HLP III.