Cholesterol levels in high‐density lipoprotein (HDL) of transgenic mice overexpressing human apolipoprotein A1 (apoAI), a des‐(190‐243)‐apoAI deletion mutant or an apoAI‐(I‐189)‐apoAII‐(12‐77) chimera were 2.8‐fold (P<0.001), 1.3‐fold (P<0.05) and 2.2‐fold (P<0.001) higher than in control mice, respectively. Human apolipoprotein levels in apoAI and in apoAI‐(1–189)‐apoAII‐(12–77) transgenic mice were 5.2‐fold and 3.5‐fold higher than in des‐(190–243)‐apoA1 transgenic mice, whereas their HDL cholesterol levels were 2.1‐fold and 1.6‐fold higher. PAGE of HDL isolated by ultracentrifuga‐tion revealed that murine HDL migrated as 9.6‐nm and 7.2‐nm particles. Overexpression of human apoAI and apoAI‐(1‐189)‐apoAII‐(12‐77) resulted in the production of polydisperse HDL (9.6, 9.2, 8.4 and 7.2 nm) particles, whereas overexpression of des‐(190–243)‐apoAI primarily resulted in an increase of 7.2‐nm particles. The fractional catabolic rates of human apoAI and apoAI‐(1‐189)‐apoAII‐(12‐77) were very similar, whereas that of des‐(190‐243)‐apoAI was 4.9‐fold higher. The endogenous production rates of human apoAI, des‐(190‐243)‐apoAI and apoAI‐(1‐189)‐apoAII‐(12‐77) in transgenic mice were very similar. It is concluded that deletion of the carboxy‐terminal domain of apoAI reduces its lipoprotein association, resulting in the production of small, phospholipid‐rich HDL particles that are cleared more rapidly. Substitution of the carboxy‐terminal helices of apoAI with helices of apoAII restores lipoprotein association, resulting in the production of HDL, which migrates as human HDL3 and HDL2. Although the carboxy‐terminal domain of the chimera contained more than 80% of the amino acid sequence of apoAII, its HDL‐distribution profile in transgenic mice was very similar to that of human apoAI. This study demonstrates the importance of the helical structure of apoAI of the carboxy‐terminal domain of apoAI, rather than of its exclusive amino acid sequence, in HDL metabolism.