We explored quantitative seedling stage resistance to barley leaf rust caused by Puccinia hordei Otth using a genetical genomics approach. We conducted a microscopic investigation of the progression of fungal infection on the barley cultivars Steptoe (St) and Morex (Mx) and identified 18 hours post infection (hpi) as a key time point in the interaction. We then recorded RNA transcript abundance corresponding to each probe on a 15K Agilent custom barley microarray in St and Mx 18hpi with P. hordei and mock-inoculated seedlings. A combined total of 1154 genes were identified as being Ph-responsive (up- or down-regulation) among the two cultivars and 1037 genes were differentially expressed between St and Mx in Ph-infected seedlings. We then examined mRNA transcript abundance at 18 hpi in 144 doubled haploid (DH) lines of the St/Mx doubled haploid (DH) reference mapping population. Normalized ratios from72 distant-pair hybridisations were used to map the genetic determinants of variation in transcript abundance by expression-QTL (eQTL) mapping. 9557 genes exhibited 1 to 6 significant eQTL (p≤0.001) culminating in a total of 15685 eQTL. We show that, in this experiment, eQTL with LOD scores of >10 are most often located close to their structural genes. Re-examination of available rust resistance scores on the St/Mx DH population using the same statistical model as employed for eQTL analysis identified four previously reported, and one additional, phenotypic QTL (pQTL). Correlation analysis revealed transcript abundance to be significantly (p≤0.001) correlated with resistance for 128 genes, of which 89 had eQTL co-located with one of the five pQTL. Differential transcript abundance in the parental lines and conservation of synteny with rice allowed us to prioritise six genes as candidates for the pQTL with the strongest effect, Rphq11.