The　dependence　of　the　interaction　between　bovine　serum　albumin　(BSA)　and　two　cinchona　alkaloids,　quinine　(QN)　and　quinidine　(QD),　on　the　absolute　configuration　of　these　stereoisomers　has　been　comprehensively　studied.　The　FTIR　spectra　showed　that　QN　and　QD　interacted　with　both　CO　and　C-N　groups　of　BSA,　resulting　in　changes　to　the　secondary　structure　of　the　protein.　Fluorescence　quenching　of　BSA　by　the　stereoisomers　revealed　lower　efficiency　for　QD　in　quenching　the　Trp　emission　of　BSA　when　compared　to　QN.　Further　analysis　accurately　described　the　different　binding　behaviors　and　recognition　discrepancies　of　QN　and　QD　towards　BSA,　which　was　reflected　through　binding　affinities,　driving　forces,　energy　changes　and　conformational　changes　during　the　ligand-protein　interactions.　Synchronous　fluorescence　further　proved　that　QD　was　farther　from　Trp　and　Tyr　than　that　of　QN.　This　work　could　provide　basic　data　for　clarifying　the　binding　interaction,　metabolism　and　distribution　of　cinchona　alkaloid　stereoisomers　in　vivo.　©　2015　Elsevier　Ltd.　All　rights　reserved.