When stimulated, rat serosal mast cells degranulate and secrete a cytoplasmic neutral protease, chymase. We studied the fragmentation of apolipoprotein (apo) A-I during proteolysis of HDL 3 by chymase, and examined how chymase-dependent proteolysis interfered with the binding of eight murine monoclonal antibodies (Mabs) against functional domains of apoA-I. Size exclusion chromatography of HDL 3 revealed that proteolysis for up to 24 h did not alter the integrity of the ␣ -migrating HDL, whereas a minor peak containing particles of smaller size with pre  mobility disappeared after as little as 15 min of incubation. At the same time, generation of a large (26 kDa) polypeptide containing the N-terminus of apoA-I was detected. This large fragment and other medium-sized fragments of apoA-I produced after prolonged treatment with chymase were found to be associated with the ␣ HDL; meanwhile, small lipid-free peptides were rapidly produced. Incubation of HDL 3 with chymase inhibited binding of Mab A-I-9 (specific for pre  1 HDL) most rapidly (within 15 min) of the eight studied Mabs. This rapid loss of binding was paralleled by a similar reduction in the ability of HDL 3 to induce high-affinity efflux of cholesterol from macrophage foam cells, indicating that proteolysis had destroyed an epitope that is critical for this function. In sharp contrast, prolonged degradation of HDL 3 by chymase failed to reduce the ability of HDL 3 to activate LCAT, even though it led to modification of three epitopes in the central region of apoA-I that are involved in lecithin cholesterol acyltransferase (LCAT) activation. This differential sensitivity of the two key functions of HDL 3 to the proteolytic action of mast cell chymase is compatible with the notion that, in reverse cholesterol transport, intactness of apoA-I is essential for pre  1 HDL to promote the high-affinity efflux of cellular cholesterol, but not for the ␣ -migrating HDL particles to activate LCAT. -Lee, M., P. Uboldi, D. Giudice, A. L. Catapano, and P. T. Kovanen. Identification of domains in apoA-I susceptible to proteolysis by mast cell chymase: implications for HDL function. J. Lipid Res. 41: 975-984.Supplementary key words ␣ -and pre  -migrating HDL • monoclonal antibodies • LCAT • cellular cholesterol efflux • proteolysis of apoA-I