We used three human apolipoprotein (apo) E targeted replacement mouse lines, each expressing one of the three common human apoE isoforms to study the pattern of apoE expression in the central nervous system (CNS). Immunocytochemistry on brain sections from all three lines of targeted replacement mice, wild type mice, African green monkeys, and humans show a predominantly glial pattern of apoE expression. The levels of human apoE protein in hippocampus and frontal cortex were similar between targeted replacement mice and non-demented human tissue. Within a given brain region, the levels of apoE were very similar amongst all three isoforms, which contrasts sharply with plasma, where apoE2 levels are 16-fold higher than apoE3 and E4 levels. Across brain regions, cerebellar apoE levels were significantly higher than cerebral apoE levels. In conclusion, we provide detailed analysis of a human apoE animal model system that recapitulates both the pattern and level of apoE expression in non-demented humans. The neurobiology of human apoE isoforms can now be studied in both the normal and post-injury state, since all apoE regulatory sequences are intact. Finally, the differences in apoE levels we observed may explain the regional vulnerability of neuronal degeneration in Alzheimer's disease.