Fusarium verticillioides is the primary fungus that causes Fusarium ear rot (FER) of maize. Infection results in reduced grain yield and quality due to moulding and the contamination of grain with toxic compounds namely fumonisins. Resistance to fungal infection and fumonisin accumulation in maize and maize grain is governed at different levels. In this study, the structural, physico-chemical and genetic basis of resistance to F. verticillioides was investigated in two, replicated field trials at Potchefstroom and Vaalharts in South Africa. Phenotypic data (silk length, husk coverage, pericarp thickness hundred-kernel mass and kernel hardness), physico-chemical data (kernel pH, moisture content, total nitrogen and carbon as well as phenolic acid content) and the expression of pathogenesis-related-5 gene (PR5) and peroxidase gene expression was evaluated in 15 commercial cultivars under artificially inoculated and natural infection conditions. The data were correlated to FER severity, fumonisin accumulation and fungal DNA (referred to as infection indicators). Disease development and fumonisin contamination in Vaalharts was significantly more than in Potchefstroom. There were no significant correlations (r=≥0.60) between phenotypic characteristics and infection indicators. Kernel pH was the most important trait associated with disease development and was negatively correlated (between r=-0.58 and r=-0.75) to all infection indicators. PR5 gene expression had significant positive correlations (r=0.69 and r=0.72) with the fungal and fumonisin levels, respectively. This study presents of the first data demonstrating the use of gene expression in identifying FER/fumonisin-resistant plant material and could aid breeders and growers in selecting resistant material more effectively.