The proprotein convertase subtilisin/kexin-type 9 (PCSK9), which promotes degradation of the hepatic low density lipoprotein receptor (LDLR), is now recognized as a major player in plasma cholesterol metabolism. Several gain-of-function mutations in PCSK9 cause hypercholesterolemia and premature atherosclerosis and thus, inhibition of PCSK9-induced degradation of the LDLR may be used to treat this deadly disease. Herein, we discovered an endogenous PCSK9 binding partner by Far Western blotting, co-immunoprecipitation and pull-down assays. Following 2D gel electrophoresis and mass spectrometry analysis we demonstrated that PCSK9 binds to a ~33 kDa protein identified as Annexin A2 (AnxA2), but not to the closely related Annexin A1. Furthermore, our functional LDLR assays and shRNA studies show that AnxA2 and the AnxA2/p11- complex could prevent PCSK9-directed LDLR degradation in HuH7, HepG2 and CHO cells. Immunocytochemistry revealed that PCSK9 and AnxA2 co-localize at the cell surface indicating a possible competition with the LDLR. Structure-function analyses demonstrated that the C-terminal cysteine-histidine rich domain of PCSK9 interacts specifically with the N-terminal repeat R1 of AnxA2. Mutational analysis of this 70 amino acid long repeat indicated that the RRTKK81 sequence of AnxA2 is implicated in this binding as its mutation to AATAA81 prevents its interaction with PCSK9. To our knowledge, this work constitutes the first to show that PCSK9 activity on LDLR can be regulated by an endogenous inhibitor. The identification of the minimal inhibitory sequence of AnxA2 should pave the way towards the development of PCSK9 inhibitory lead molecules for the treatment of hypercholesterolemia.