Idiopathic Eosinophilic Enteritis (IEE) is an intestine disease that affects absorption of nutrients and performance. Hens of a commercial breeding layer line and its two reciprocal crosses with another line were recorded for IEE related traits and genotyped for over 40,000 genetic markers across the genome. Whole genome association analysis was performed on 288 daughters from high and low incidence sire families. Single marker association analyses of IEE incidence in separate lines showed consistent significant regions on chromosomes 4 and 5 (p<0.001). Simultaneous analyses of all SNPs in all 3 lines using Bayesian whole genome selection methods indicated evidence of associations on chromosomes 1, 2 and 4 for additive effects and on chromosome 5 for dominance effects. Line specific regions also appeared on chromosome Z. With further investigation, these results can be used to develop genetic markers to select against this disease and to understand its genetic basis.