Fusarium wilt has developed as a major threat to cotton production in Australia. The pathogen can be dispersed as seed-borne inoculum and may survive within the seed between the kernel and the seed coat. With the increasing distribution and prevalence of Fusarium wilt it has become more difficult to locate ‘clean’ areas for seed production. Fourteen seed treatment fungicides were evaluated for the control of seed-borne inoculum of the pathogen. Only TCMTB, carbendazim and the current Australian standard cotton seed treatment, PCNB-metalaxyl gave repeated complete control in the Petri plate tests. When PCNB and metalaxyl were tested separately only metalaxyl gave repeated complete control. The unexpected efficacy of metalaxyl is discussed.