Cyclooxygenase (COX; prostaglandin H synthase, prostaglandin endoperoxidase) is the key enzyme in the synthesis of the prostaglandin and thromboxane families of eicosanoid mediators, and is the target for the nonsteroidal anti-inflammatory drugs (NSAIDs). The identification of an inducible COX isoform, COX-2, and the demonstration of its specific expression at sites of inflammation suggested that it may provide a useful therapeutic target for novel anti-inflammatory drugs. Inhibition of an enzyme that is not expressed in most healthy tissues would potentially avoid most of the adverse effects associated with NSAIDs, which target a constitutively expressed isoform, COX-1. The development of novel ‘super aspirins’ with high selectivity towards the inhibition of COX-2 showed that this hypothesis was well-founded and that high levels of these drugs could be tolerated without these serious adverse effects. The first two of these new generation NSAIDs, celecoxib and rofecoxib, are now in clinical use.More recently, however, concern has been expressed that COX-2 inhibition may in fact have a number of potential, previously hidden, pitfalls. These have arisen from the demonstration that COX-2 induction is not exclusively associated with the onset of an inflammatory reaction, with expression limited to inflammatory sites. In fact, COX-2 is expressed more chronically, and is also seen during the resolution of inflammation and in areas of wound-healing. The application of COX-2-selective inhibitors during these periods has been shown to be deleterious in that resolution of inflammation is delayed, gastric ulcer healing is delayed and, in some patients, ulcers have been shown to progress further to perforation. The suggestion has now been made that, in these situations, COX-2 may help resolve the pathology, perhaps by generating alternative series of prostaglandins such as the cyclopentenone prostaglandins. The finding that these prostaglandins can affect proteins by direct chemical modifications as well as having their own receptor families has rekindled debate on the deleterious and beneficial effects of prostanoids, and the implications of inhibiting the production of these mediators, in the body.Therefore, in this review we discuss the role of COX-2 in inflammation and the potential adverse effects of its inhibition.