Isolation of high density lipoproteins (HDL) for structural and functional studies typically relies on ultracentrifugation techniques， which are time-consuming and difficult to scale. With emerging interest in the clinical relevance of HDL structure and function to cardiovascular disease， a significant gap exists between current and desirable sample preparation throughput. To enable proteomic studies of HDL with large clinical cohorts， we have developed an affinity enrichment approach that relies on the association of histidine-tagged， lipid free ApoA-I with HDL followed by standard metal chelate chromatography. Characterization of the resulting affinity-enriched ApoA-I associated lipoprotein (AALP) pool using biochemical， electrophoretic， and proteomic analysis demonstrates that the isolated material is closely related in structural features， lipid content， protein complement， and relative protein distribution to HDL isolated by ultracentrifugation using sequential density adjustment. The simplicity of the method provides avenues for high-throughput analysis of HDL associated proteins.