Rp1-D21 is a maize auto-active resistance gene conferring a spontaneous hypersensitive defense response (HR) of variable severity depending on genetic background. We report an association mapping strategy based on the Mutant Assisted Gene Identification and Characterization (MAGIC) approach to identify naturally-occurring allelic variants associated with phenotypic variation in HR. Each member of a collection of 231 diverse inbred lines of maize constituting a high-resolution association mapping panel were crossed to a parental stock heterozygous for Rp1-D21 and the segregating F(1) generation testcrosses were evaluated for phenotypes associated with lesion severity for two years at two locations. A genome-wide scan for associations with HR was conducted with 47,445 SNPs using a linear mixed model that controlled for spurious associations due to population structure. Since the ability to identify candidate genes and the resolution of association mapping are highly influenced by linkage disequilibrium (LD), we examined the extent of genome-wide LD. On average marker pairs separated by more than 10 kbp had an r(2) value of less than 0.1. Genomic regions surrounding SNPs significantly associated with HR traits were locally saturated with additional SNP markers in order to establish local LD structure and precisely identify candidate genes. Six significantly associated SNPs at five loci were detected. At each locus, the associated SNP was located within or immediately adjacent to candidate causative genes predicted to play significant roles in the control of programmed cell death and especially in ubiquitin pathway-related genes.