Intermediate conductance calcium-activated potassium channels (IK1) are involved in important physiological and pathophysiological processes such as cell volume regulation, trans epithelial secretion, T lymphocyte activation, proliferation of cancer cells and cell migration. On a cellular level, IK1 channels are important regulators of cell migration. Their inhibition impairs migration. Immunofluorescent labeling of IK1 channels reveals a punctuate distribution of IK1 channels in the plasma membrane. We used quantum dots (QDs) to label fixed MDCK-F cells that were transfected with the human IK1 channel (hIK1) containing an HA-tag in the extracellular S3-S4 linker for single molecule detection. hIK1 channels were stained from the extracellular side with an a-HA antibody and a secondary antibody labelled with 565 nm QDs. The density of QDs and thereby the number of channel proteins is 1.53 ± 0.15 per mm. This number is in the same order of magnitude as that derived from patch clamp experiments. To verify that a single QD corresponds to a single channel protein we applied dual-colour labeling (565 nm QDs and 655 nm QDs). It shows that most of the QDs (~ 94%) are single and one QD is bound to one channel protein. Our technique will allow the analysis of the distribution of potassium channel proteins on the single molecule level.