PURPOSE. To evaluate apolipoprotein (Apo) gene expression in native human retinal pigment epithelium (RPE) and neurosensory retina and to detect apolipoproteins within age-related, extramacular drusen. METHOD. Drusen were isolated manually from 10 eyes of 10 donors (age range, 58-93 years) with grossly normal maculas that were preserved in 4% paraformaldehyde within 6 hours of death. In cryosections of druse-enriched pellets (6-57 drusen per eye), the Apos A-I, A-II, B, C-I, C-II, C-III, E, and J were detected by indirect immunofluorescence. Two graders assessed the prevalence and pattern of immunoreactivity. mRNA transcripts were detected by reverse-transcription polymerase chain reaction (RT-PCR), with human hepatoma HepG2 cells as the positive control. RESULTS. Extramacular drusen were classified in two groups on gross appearance: transparent with a reflective shell and cloudy. The proportion of the latter increased significantly with age. All Apos examined were detectable, in descending order of prevalence: ApoE (99.5%), J (99.5%), C-I (93.1%), B (80.4%), A-I (61.0%), A-II (59.2%), C-II (57.7%), and C-III (16.6%). Immunoreactivity was either diffusely distributed throughout the drusen (56.7%), confined to the druse rim (16.0%), or both (21.2%). Six percent displayed evidence of organized substructure reminiscent of active remodeling. The proportion of diffusely labeled drusen decreased significantly with age for ApoE (P = 0.034) and ApoE/C-I combined (P = 0.027). RT-PCR products for Apos C-I, C-II, E, and J were found in retina and RPE; for ApoA-II in the retina only. The ApoC-III message was undetectable. CONCLUSIONS. To an emerging model of an RPE-secreted large lipoprotein particle implied by previous work, this study adds ApoC-I and ApoC-II, major modulators of lipoprotein lipase activity, and confirms previously demonstrated Apos A-I, B-100, and E. It is possible that a neutral lipid-rich druse shell containing Apos will be visible in the living fundus. Copyright © Association for Research in Vision and Ophthalmology.