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A survey was carried out during the 1999/2000 cotton season in the seed multiplication areas to investigate the status of cotton wilts there. The initial cotton seed multiplication was carried in isolated areas referred to as segregated areas (Segs. 1). These were selected in Pallisa, Kamuli, Apac, Kasese, Lira and Soroti districts. It was found out that Fusarium wilt incidence was highest in Pallisa followed by Kamuli districts with 64.4% and 43.5% of the fields surveyed having Fusarium wilt. However the disease was not very severe, with most of the infested fields having small patches of less than 2% plants affected. The rest of the Segs. 1 areas had isolated incidences of wilts which was identified as Verticillium wilt. In Pallisa and Kamuli Fusarium wilt was found in predominantly sandy loam soils which also had high root knot nematode infestation. In view of the findings the paper discusses and proposes some key research areas in regard to the wilts problem.