Tomato is an important vegetable crop worldwide and Fusarium wilt is a significant disease of tomato in many countries. One hundred and fifty three diverse tomato genotypes collected from local and exotic sources were screened for resistance to F. solani in the greenhouse. Significant variation in genotype response to inoculation was observed. The organic metabolite profiles of resistant and susceptible genotypes were assessed to determine the basis of resistance. Significant genetic variation was observed for ABA, malic acid, citric acid, fructose, glucose, sucrose, L-proline and myo-inositol. The disease treatment produced significant changes in fructose, glucose, proline and sucrose and significant genotype-by-treatment interaction was observed for ABA, citric acid, fructose, glucose, malic acid and sucrose, indicating that genetic improvement of these traits is feasible. Disease incidence was strongly associated with citric acid (R 2 = 0.84), sucrose (R 2 = 0.72) and L-proline (R 2 = 0.76). Principal component analysis confirmed that citric acid and L-proline were important in determining plant disease response. Genetic variation for Fusarium wilt resistance can be used to develop new tomato cultivars with improved disease resistance.