Background and purpose: Pentamidine is a drug used in treatment of protozoal infections. Pentamidine treatment may cause sudden cardiac death by provoking cardiac arrhythmias associated with QTc prolongation and U-wave alterations. This proarrhythmic effect was linked to inhibition of hERG trafficking, but not to acute block of ion channels contributing to the action potential. Because the U-wave has been linked to the cardiac inward rectifier current (IK1), we examined the action and mechanism of pentamidine-mediated IK1 block. Experimental approach: Patch clamp measurements of IK1 were made on cultured adult canine ventricular cardiomyocytes, KIR2.1-HEK293 cells and KIR2.x inside-out patches. Pentamidine binding to cytoplasmic amino acid residues of KIR2.1 channels was studied by molecular modelling. Key results: Pentamidine application (24 h) decreased IK1 in cultured canine cardiomyocytes and KIR2.1-HEK293 cells under whole cell clamp conditions. Pentamidine inhibited IK1 in KIR2.1-HEK293 cells 10 min after application. When applied to the cytoplasmic side under inside-out patch clamp conditions, pentamidine block of IK1 was acute (IC50 = 0.17 mM). Molecular modelling predicted pentamidine-channel interactions in the cytoplasmic pore region of KIR2.1 at amino acids E224, D259 and E299. Mutation of these conserved residues to alanine reduced pentamidine block of IK1. Block was independent of the presence of spermine. KIR2.2, and KIR2.3 based IK1 was also sensitive to pentamidine blockade. Conclusions and implications: Pentamidine inhibits cardiac IK1 by interacting with three negatively charged amino acids in the cytoplasmic pore region. Our findings may provide new insights for development of specific IK1 blocking compounds.