In a field in Australia, the influence of growing different rotation crops on the level of Fusarium oxysporum f.sp. vasinfectum (Fov) in the soil was monitored over three years in a summer field crop rotation experiment. In the 2001-02 and 2002-03 seasons of the trial, the same crop was grown on the same plot. The maize plots were a forced fallow during 2002-03. In 2003-04, the entire trial was oversown with cotton cv. Nu Emerald RR. Mung bean plots were replanted with Sicot 14B six weeks later. In glasshouse pot trials, soil naturally infested with Fov was used to examine different rotation options over five crop cycles with cotton oversown across all treatments in the final cycle. In the field, significantly more cotton plants survived until maturity following a bare fallow rotation compared to cotton plants grown following either maize, cotton or sorghum crops. The greatest percentage of cotton plant death and severity of disease in cotton occurred where soyabean or mung bean crops had previously been grown. In the glasshouse, rotation cycles that included a fallow treatment either one or two crops before growing cotton generally resulted in less severe Fusarium wilt (lower MDI) compared to cycles where a fallow treatment was not included occurred early in the cycle. Crops with larger root systems (sunflower, broccoli, lucerne, maize, sorghum) had more disease (higher MDI) in the following cotton compared to crops with smaller root systems (fallow, chickpea, field pea, millet, pigeon pea), after these crops had been grown for four continuous cycles, reflecting the role of residue and organic matter in pathogen survival and disease incidence. Fov has been isolated from mature plants growing in these pot trials including sunflower (5%); maize (4%); sorghum (3%) (roots only); mung bean (24%); field pea (20%); vetch (20%); pigeon pea (12%); chickpea (4%); and lucerne (4%) (stems and roots). Further research into rotation options and the roles of crop residue, organic matter and green manuring of crops in relation to pathogen survival are discussed.