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Participatory variety selection trials involving farmers in northern Uganda were conducted in order to assess and select cowpea lines with desirable attributes and tolerance to virus infection. The trials were set up on-farm in farmers’ field in the districts of Apac, Lira and Pader in two seasons of 2009A and 2009B. In 2009A, with involvement of farmers, 36 cowpea lines and one local check were evaluated and selected for desirable attributes. This resulted in selection of thirteen cowpea lines that were further evaluated with one local check in 2009B season following a randomised complete block design. In this participatory approach, farmers used different criteria to assess cowpea linesat the vegetative and maturity crop growth stages. Major selection criteria included the leaf appearance, leaf texture, leaf and grain taste, yield potential, pod and seed size. In the three districts farmers provided valuable knowledge in identifying the lines of preference and therefore, indicating their competence in assessing and selecting the cowpea lines. Farmers preferred the high yielding, big pod and seed sizes, virus tolerant and tasty lines. Overall, the results showed that farmers had knowledge to make decision of the preferred lines and this resulted in selection of eight more superior cowpea lines compared to the ones currently grown by farmers. The study revealed that using participatory approach also shortened the process of identifying the lines because farmers were able to quickly select the lines with traits they preferred.