Suppressive subtractive hybridization (SSH) was used to analyse the muscle transcriptome and identify genes affecting meat quality within an Italian pig population of Large White and Landrace purebred individuals. Seven phenotypes were recorded at slaughter: dorsal fat thickness, ham fat thickness, ham fat coverage, muscle compactness, marbling, meat colour and colour uniformity. Two subtractive libraries were created from longissimus dorsi tissue of selected pigs with extreme phenotypes for meat quality. Eighty-four differentially expressed ESTs were identified, which showed homology to expressed pig sequences and/or to genomic pig sequences produced within the pig genome project. Sixty-eight sequences were mapped on the pig genome, and most of these sequences co-localized with the same chromosomal positions as QTLs that have been previously identified for meat quality. Thirty sequences, including eight matching known genes previously related to muscle metabolic pathways, were selected to statistically validate their differential expression. Association analysis and t-test results indicated that 28 ESTs of the 30 analysed were associated with phenotypes investigated here and have significant differential expression levels (P ≤ 0.05) between the two tails of the phenotypic distribution.