Baseline epidemiological investigations on lymphatic filariasis were conducted for the first time in Uganda in 3 communities in the districts of Lira (Alebtong area), Soroti (Lwala area) and Katakwi (Obalanga area), located to the north of Lake Kyoga at an altitude of 1000-1100 m above sea level. Individuals from the communities were examined, in April-August 1998, for Wuchereria bancrofti specific circulating antigen (by ICT card test), microfilaraemia (by counting chamber and stained blood-smear techniques) and chronic clinical manifestations of lymphatic filariasis. Endophilic mosquitoes were sampled and dissected for filarial larvae. Prevalences of circulating filarial antigen positivity were 29%, 18% and 30% in the Alebtong, Lwala and Obalanga communities, respectively. Microfilaria (mf) prevalences were 18%, 9% and 21%, and geometric mean mf intensities among mf-positive individuals were 306, 171 and 402 mf/mL blood, in the same communities. Examination of stained blood smears revealed mf of both W. bancrofti and Mansonella perstans, but more than 80% of mf-positive individuals harboured the first of these parasites. Prevalences of hydrocoele in adult (> or = 20 years) males were 28%, 7% and 17%, and prevalences of limb elephantiasis in adults were 9%, 4% and 4%, in the Alebtong, Lwala and Obalanga communities, respectively. Anopheles gambiae s.l. (mainly An. gambiae s.s.) and An. funestus were common in all 3 communities, and showed W. bancrofti infectivity rates of 1.1-1.7% and 1.3-2.9%, respectively. It is concluded that lymphatic filariasis is highly endemic in these high-altitude areas of Uganda, with An. gambiae s.l. and An. funestus being the main vectors.