Cystic Fibrosis (CF), the most common lethal genetic disease of Caucasians, is caused by mutations in the gene that encodes the cystic fibrosis transmembrane conductance regulator (CFTR). In relation to the lungs, this disease is characterised by mucus build-up, airway inflammation and microbial infection. Pseudomonas aeruginosa is the most dominant bacterial pathogen causing chronic lung infections in CF patients and is a significant contributor to morbidity and mortality in these individuals. P. aeruginosa is a versatile opportunistic pathogen producing an arsenal of virulence factors that enhance survival within the host by sequestering nutrients, contributing to tissue damage and evading the host immune response. In this study, we report data from transcriptome profiling of epithelial cells in response to infection with wild-type and mutant strains of P. aeruginosa. The CFTE29o- cell-line, derived from tracheal epithelium from a CF patient is homozygous for the most common CFTR mutation, delta F508. P. aeruginosa was co-cultured with these cells at a multiplicity of infection of 50:1. Total RNA was extracted from CFTE29o- cells 1.5h post-infection and prepared for Affymetrix GeneChip® analysis as per manufacturer’s instructions. Changes in gene expression in cells co-cultured with wild-type or mutant bacteria relative to no bacteria were analysed using GeneSight® software (Biodiscovery). mRNA transcript levels that changed by at least 2-fold in response to infection were considered significant. In response to infection with wild-type P. aeruginosa, approximately 3% of the 22,215 represented genes showed a significantly altered expression 1.5h post-infection. Initial analysis indicates that the expression of genes involved in transcriptional regulation (ATF3, IFR5, MADH6, COPEB and KLF2), cytoskeletal organisation (ARHB, CDC42) and inflammatory response (interleukins, chemokines and TNF superfamily members) are altered in response to P. aeruginosa. To further investigate the differential regulation of a number of transcription factors at this early infection timepoint, temporal expression of these and additional genes in response to infection is being assessed. These changes in the expression profile of CFTE29o- cells undergoing infection indicate novel response mechanisms upon infection with P. aeruginosa. Investigation of the host response to P. aeruginosa strains, mutated in key virulence-related genes, has also been carried out and comparative analysis may further elucidate the role of specific bacterial regulatory proteins in microbial infection.