BACKGROUND: Ivermectin has been used for onchocerciasis control since 1987. Because of the long-term use of this drug and the development of resistance in other nematodes, we have assessed Onchocerca volvulus burdens, effectiveness of ivermectin as a microfilaricide, and its effect on adult female worm reproduction. METHODS: For the first phase of the study, 2501 individuals in Ghana, from 19 endemic communities who had received six to 18 annual rounds of ivermectin and one ivermectin naive community, were assessed for microfilarial loads 7 days before the 2004 yearly ivermectin treatment, by means of skin snips, and 30 days after treatment to assess the ivermectin microfilaricidal action. For the second phase, skin snips were taken from 342 individuals from ten communities, who were microfilaria positive at pretreatment assessment, on days 90 and 180 after treatment, to identify the effects of ivermectin on female worm fertility, assessed by microfilaria repopulation. FINDINGS: 487 (19%) of the 2501 participants were microfilaria positive. The microfilaria prevalence and community microfilarial load in treated communities ranged from 2.2% to 51.8%, and 0.06 microfilariae per snip to 2.85 microfilariae per snip, respectively. Despite treatment, the prevalence rate doubled between 2000 and 2005 in two communities. Microfilaria assessment 30 days after ivermectin treatment showed 100% clearance of microfilaria in more than 99% of people. At day 90 after treatment, four of ten communities had significant microfilaria repopulation, from 7.1% to 21.1% of pretreatment counts, rising to 53.9% by day 180. INTERPRETATION: Ivermectin remains a potent microfilaricide. However, our results suggest that resistant adult parasite populations, which are not responding as expected to ivermectin, are emerging. A high rate of repopulation of skin with microfilariae will allow parasite transmission, possibly with ivermectin-resistant O volvulus, which could eventually lead to recrudescence of the disease.