Purpose: Breeding for gibberella ear rot resistance have been challenging due to the high complexity of the trait. The current study attempts to characterize defence responses to Fusarium graminearum infection in two maize inbred lines with different levels of resistance to the pathogen. Methods: RNA was extracted from developing kernels of two inbred lines, which had been either fungal (F. graminearum DAOM180378) or mock inoculated 11 days post sibcrossing, using a guanidine isothiocyanate method and ultra-centrifugation with cesium chloride. Isolated RNA was used to quantify whole genome gene expression using RNA-seq (Illumina TruSeq RNA library prep kit v2, Illumina HiSeq 2000). Paired end reads generated from RNA-seq were trimmed of adaptors and low quality reads, aligned with the B73 reference genome sequence version 2, expression levels (TPM) were computed and differential gene expression analysis were performed using CLC Genomics Workbench version 9. Results: Gene transcripts responding to fungal infection were captured by comparing gene expression levels in mock and fungal inoculated maize ears and gene ontology terms associated with significantly up-regulated gene transcripts were determined for each inbred. More genes were up regulated in the susceptible inbred relative to the resistant inbred, many of which are associated with oxidation-reduction processes potentially causing earlier programmed cell death in the susceptible inbred. Conclusions: This information helped to identify gene transcripts that were relevant in defense responses with potential applicability in routine breeding efforts and to propose an effective GER resistance mechanism. Overall design: The experiment consisted of 16 RNA samples from two inbreds (B73 and CO441) tested over two years (2004 and 2006), two treatments (mock and fungal) and two sampling times (1 and 2 days after inoculation).