Top-down proteomics (TDP) allows precise determination/characterization of the different proteoforms derived from the expression of a single gene. In this study, we targeted apolipoprotein A-I (ApoA-I), a mediator of high-density-lipoprotein cholesterol efflux (HDL-E), which is inversely associated with coronary heart disease risk. Absolute ApoA-I concentration and allelic variation only partially explain inter-individual HDL-E variation. Therefore, we hypothesize that differences in HDL-E are associated with the abundances of different ApoA-I proteoforms. Here, we present a targeted TDP methodology to characterize ApoA-I proteoforms in serum samples and compare their abundances between individuals. We characterized eighteen ApoA-I proteoforms using selected-ion monitoring coupled to electron-transfer dissociation mass spectrometry. We then compared the abundances of these proteoforms between two groups of four participants, representing the individuals with highest and lowest HDL-E values within the Chicago Healthy Aging Study (n=420). Six proteoforms showed significantly (p<0.0005) higher intensity in high HDL-E individuals: canonical ApoA-I [fold difference (fd)=1.17], carboxymethylated ApoA-I (fd=1.24) and, with highest difference, four fatty acylated forms: palmitoylated (fd=2.16), oleoylated (fd=2.08), arachidonoylated (fd=2.31) and one bearing two modifications: palmitoylation and truncation (fd=2.13). These results demonstrate translational potential for targeted TDP in revealing, with high sensitivity, associations between inter-individual proteoform variation and physiological differences underlying disease risk.