The antiprotozoal drug pentamidine inhibits two types of cardiac rectifier potassium currents, which can precipitate life-threatening arrhythmias. Here, we use pentamidine as a tool to investigate whether a single drug affects trafficking of two structurally different potassium channels by identical or different mechanisms, and whether the adverse drug effect can be suppressed in a channel specific fashion. Whole cell patch clamp, Western blot, real time PCR, and confocal laser scanning microscopy were used to determine potassium current density, ion channel protein levels, mRNA expression levels, and subcellular localization, respectively. We demonstrate that pentamidine inhibits delayed (I(Kr)) and inward (I(K1)) rectifier currents in cultured adult canine cardiomyocytes. In HEK293 cells, pentamidine inhibits functional K(v)11.1 channels, responsible for I(Kr), by interfering at the level of full glycosylation, yielding less mature form of K(v)11.1 at the plasma membrane. In contrast, total K(IR)2.1 expression levels, underlying I(K1), are strongly decreased, which cannot be explained from mRNA expression levels. No changes in molecular size of K(IR)2.1 protein were observed, excluding interference in overt glycosylation. Remaining K(IR)2.1 protein is mainly expressed at the plasma membrane. Inhibition of lysosomal protein degradation is able to partially rescue K(IR)2.1 levels, but not those of K(v)11.1. We conclude that 1) a single drug can interfere in cardiac potassium channel trafficking in a subtype specific mode and 2) adverse drug effects can be corrected in a channel specific manner.