Mycotoxins are significant food contaminants with severe negative impacts on public health, food security and agriculture-based economies.  They affect a wide range of cereals, nuts, and oilseed crops, including maize (Zea mays L). Aflatoxins are produced as secondary metabolites under conducive climatic conditions by the fungus Aspergillus flavus Link:Fr. Plant defense against pathogens is a complex process that includes the expression of an array of defense genes and the production of antimicrobial substances.   Genes encoding plant defense-related proteins include several evolutionarily conserved families with individual members differing widely in occurrence and activity; one such family includes the pathogenesis-related proteins PR-3, -4, -8, and -11 endochitinases, which are hydrolytic enzymes that catalyze the degradation of chitin, a major component of insect skin and fungal cell walls.  Several classes and isoforms of chitinases with different structures, substrate specificities, intracellular locations, and specific activities are constitutively present in plants.  A candidate gene testing pipeline has been created to validate putative A. flavus and aflatoxin accumulation resistance genes in maize.  The pipeline tests the effect of any DNA sequence in four QTL mapping populations and one association mapping population, all of which have been phenotyped under replicated field experiments for aflatoxin levels, and in some cases, ear rot and/or fungal biomass.  The objectives of this study were to characterize major chitinase genes in maize, and to test them for association to resistance to aflatoxin accumulation and A. flavus resistance in field grown maize.  Several of the chitinase sequences studied have been found to be significantly associated with decreased aflatoxin levels in maize in one or more of these populations.