Veterinary and human pharmaceuticals are an emerging category of chemical pollutants with potential to cause serious toxicity to non-target organisms. Filter-feeding aquatic organisms such as mussels are especially threatened. In this study, the blue mussel, Mytilus edulis, was exposed to two doses (0.2 mg/L and 1 mg/L) of the anti-inflammatory diclofenac. Effects on the gill, the principal feeding organ of mussels, were investigated. It was noted that, while no effect was evident on gill glutathione transferase or catalase activities, there was a tissue-specific increase in glutathione reductase activity and reduction in total protein thiol groups. Two dimensional electrophoresis was performed and some affected proteins identified by in-gel tryptic digestion and peptide mass fingerprinting. Of these, four unique proteins (caspase 3/7-4, heat-shock cognate protein 70, a predicted enolase-like protein, arginine kinase) were found to be oxidized whilst eight unique proteins (β-tubulin, actin, isocitrate dehydrogenase, arginine kinase, heavy metal-binding HIP, cytosolic malate dehydrogenase, proteasome subunit alpha type 2, Mg: bb02e05 (glyceraldehyde-3-phosphate dehydrogenase) and superoxide dismutase) were found to have altered abundance. In addition, bioinformatic analysis suggested putative identities for six hypothetical proteins which either were oxidized or decreased in abundance. These were; 78 kDa glucose-regulated protein precursor, α-enolase, calreticulin, mitochondrial H + -ATPase, palmitoyl protein thioesterase 1 and initiation factor 5a. It is concluded that diclofenac causes significant oxidative stress to gills and that this affects key structural, metabolic and stress-response proteins.