Among the terrestrial production animals, chickens are the most efficient users of energy. Apparent metabolisable energy (AME) is a measure of energy utilisation efficiency representing the difference between energy consumed and energy lost via the excreta. There are significant differences in the energy utilisation capability of individual birds that have a similar genetic background and are raised under identical conditions. It would be of benefit to poultry producers if the basis of these differences could be understood and the differences minimised. We analysed duodenal gene expression and microbiota differences in birds with different energy utilisation efficiencies. Using microarray analysis, significant differences were found in duodenal gene expression between high- and low-AME birds, indicating that level of cell turnover may distinguish different groups of birds. High-throughput sequencing of bacterial 16S rRNAgenes indicated that duodenal microbiota was dominated by Lactobacillusspecies and two operational taxonomic units, identified as lactobacilli species, were found to be more abundant (P<0.05) in low-AME birds. The present study has identified gene expression and microbiota properties that correlate with differences in AME; further studies will be required to investigate the causal relationships.