The cholesterol and lipid transporter, apolipoprotein E (ApoE), has an important although uncertain role in the pathogenesis of sporadic Alzheimer’s disease (AD). ApoE’s importance is demonstrated by the significantly increased risk of developing alzheimer’s disease between the three main alleles of APOE, ε2, ε3, ε4.  ApoEε4 is the most jeopardizing allele, conferring a dose-dependent increase to the risk for AD and reducing the mean age of onset from 84 to 68 years old in homozygous ε4 persons, compared to persons with no ε4. Whereas ε4 is second only to age in importance amongst AD risk factors, its presence is neither necessary nor sufficient to cause AD, suggesting that environmental or other genetic elements contribute to the disease.  Here we show using large-format, narrow pI range (4.7-5.9), 2D-PAGE proteomics of heparin-sepharose binding proteins from homozygous (ε2/ε2, ε3/ε3, ε4/ε4) human sera. We find no differences in total spot volumes from ApoE spot trains between heparin-Sepharose enriched sera from healthy or Alzheimer’s disease ApoE carriers. Furthermore, there were no significant differences found between ε2, ε3 or ε4 carriers of native ApoE migrating at 34 kDa.  However, a reduction-resistant variant migrating at 45 and 55 kDa were found in ε3/ε3 and e2/e2 individuals respectively.  Mass spectrometry identified these species to be complexes of ApoE, ApoAII and amyloid β. These data suggest that ApoE isoforms have unique functions that require further investigation.