Ivermectin (IVM) was first developed for use with livestock. It is now the only drug used for mass treatment of onchocerciasis. It is difficult to prove whether reports of sub-optimal responses to IVM in some Onchocerca volvulus infected patients are a result of drug resistance, as procedures typically used to examine IVM efficacy in livestock can not be performed on humans. To determine the effects of IVM on O. volvulus, one approach is to examine allele frequencies before and after treatment. Allele(s) linked to resistance may increase in frequency after repeated treatment. Mass treatment of large human populations to reduce transmission of O. volvulus will impose selection pressure for resistance. P-glycoprotein has been implicated as a candidate IVM resistance gene in nematodes. In this study, the intron-exon structure of O. volvulus P-glycoprotein (OvPGP) has been defined. The gene spans 10.6 kb, is AT-rich, contains 24 exons and a high proportion of class 0 introns. The genetic diversity of 28 loci spanning the entire OvPGP gene was examined in four O. volvulus populations from the Volta Region of Ghana. Worms collected in 1999 and 2002 from IVM treated patients showed reduced genetic polymorphism and an increase in the number of loci not in Hardy-Weinberg equilibrium. Changes in allelic patterns and a reduction in diversity at many loci in P-glycoprotein in the parasites from IVM treated patients in 1999 and 2002 suggest that IVM is imposing selection on this gene, consistent with a possible development of IVM resistance.