The ATP-binding cassette (ABC) superfamily is one of the largest protein families with representatives in all kingdoms of life. Members of this superfamily are involved in a wide variety of transport processes with substrates ranging from small ions to relatively large polypeptides and polysaccharides, but also in cellular processes such as DNA repair, translation or regulation of gene expression. For many years, the role of ABC proteins was mainly investigated for their implication in drug resistance. However, recent studies focused rather on their physiological functions for the parasite. In this review, we present an overview of ABC proteins in major protozoan parasites including Leishmania, Trypanosoma, Plasmodium, Toxoplasma, Cryptosporidium and Entamoeba species. We will also discuss the role of characterized ABC transporters in the biology of the parasite and in drug resistance.