A field survey on indigenous fruit tree species (IFTS) was conducted in Adwari subcounty, Lira district between August 2004 and March 2005. The objectives were to: determine IFTS diversity in the traditional farming system; generate a species priority list, characterize and document the values of IFTS as perceived by farmers; and develop criteria for selecting IFTS for on-farm cultivation. A questionnaire designed to capture socio-economic data was administered to 120 randomly selected respondents. Farm walks were conducted to identify and assess the proportion of farmland under IFTS. Preference ranking was used to generate a species priority list. On-farm diversity of IFTS was analyzed using Shannon–Wiener’s diversity index (H′). DAFOR scale was used to rate occurrence of IFTS on-farm. The diversity of IFTS was relatively high (H′ = 2.164) although the average proportion of farmland under IFTS cover was low (23.3 ± 5%). Vitellaria paradoxa, Vitex doniana, Anona senegalensis and Tamarindus indica were most preferred by local people. The choice of IFTS for on-farm cultivation varied from their food, medicinal to cash values. There is a need to formulate clear policies and by-laws to encourage on-farm cultivation of IFTS.