Adaptation to heat exposure is required to maintain animal welfare and productivity under high ambient temperature (AT) conditions. In this study we investigate the effects of chronic heat exposure (5 weeks at a constant temperature of 32°C) on the liver and whole blood transcriptome of brown egg layers from 2 divergent lines selected for low (R-) and high (R+) residual feed intake. The R+ and R- hens were equally distributed among 2 temperature-controlled chambers and reared under thermo-neutrality (22°C). At 28 wk of age the AT of one chamber was increased to 32°C until 33 wk of age, when 32 animals (8 per line and treatment) were slaughtered. Total RNA was obtained from the liver and blood and was sequenced using the Illumina HiSEqn 3000, yielding an average per sample of 90 million paired-end reads. The reads were mapped to the Gallus gallus-5 reference genome by STAR software and counted by RSEM software using the Ensembl V87 GTF annotation. Comparisons between the two AT groups were made using the edgeR-robust R/Bioconductor package. Patterns of AT-specific differential expression were largely shared by the two lines, and no evidence of temperature × line interactions were observed. In liver, a total of 229 differentially expressed genes (DEG) were identified (adjusted P-values < 0.05) with respectively 104 and 125 over and under expressed in the heat-exposed compared to the control group. In blood, 960 DEG were identified between the two AT groups with 479 and 481 over and under expressed. Most DEG were tissue specific, and only 18 genes were DE in both liver and blood. Ingenuity Pathway Analysis revealed that many of the DEG in liver were associated with amino acid and lipid metabolisms and energy production. Key genes involved in fatty acid β-oxidation, ketogenesis, cholesterol biosynthesis were under-expressed in the heat-exposed animals. In blood, many of the DEG were associated with cell related functions. Based on the DEG expression profile, down-regulation was observed for the PI3K/AKT, the VEGF and the PDGF signalling pathways involved in cell survival and growth, vasculogenesis and angiogenesis. Taken together, these results indicate a tissue-specific response to heat exposure.