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Abstract Background A prevalence study of Wuchereria bancrofti infection was carried out in 2014 at 4 study sites in northern Uganda using antigen and microfilaria tests. Each study site consists of a primary school and surrounding communities. These sites are inside the filariasis endemic area and have been covered by mass drug administration under the national elimination programme. However, no prevalence study had been conducted there before the present study. Without information on past and present endemicity levels, our study was meant to be an independent third-party investigation to know the latest filariasis situation. Results A total of 982 people including 570 schoolchildren (7–19 years) and 412 community people (7–25 years) were examined, all of them for filarial antigen and 695 for microfilariae. The study revealed that all subjects were negative by both methods. Conclusions It was considered that annual mass drug administrations together with anti-malarial activities such as indoor residual spraying had contributed to the reduction of the filarial infection. However, based on the past data obtained near our study sites, we cannot exclude the possibility that filarial prevalence rates in our study sites were very low or even zero originally. During the study, we encountered several patients with lower leg edema and pachydermic (elephant skin-like), mossy skin lesion of the foot. Judging from clinical features and bare-footed life-style of people in the area, non-filarial elephantiasis, possibly podoconiosis, was suspected. This elephantiasis has been reported in areas where filariasis is not endemic.