The virulence of Pseudomonas aeruginosa in contact lens-induced microbial keratitis has been linked to various extracellular and cell-associated bacterial products, such as proteases and toxins. Recently, a group of bacterial signal molecules, N-acyl-homoserine lactones (AHLs), has been reported to play an important role in the regulation of the production of several bacterial virulence factors in P. aeruginosa. The aim of this study was to determine the signal molecules produced by P. aeruginosa keratitis strains, and to elucidate any possible correlation between the production of signal molecules and the expression of phenotypic characteristics, including protease production, bacterial invasion and acute cytotoxic activity. The presence and profiles of AHLs in ocular P. aeruginosa isolates were analysed by a combination of thin-layer chromatography and bioassay. All 17 keratitis isolates produced AHLs. There were differences both in the amounts and the types of AHL production in the various phenotypes of isolates. High levels of AHLs were found among the isolates with high protease activity and invasiveness. Acutely cytotoxic isolates displayed low AHL and protease activities. Invasive strains were more common than cytotoxic strains from keratitis patients. These results suggest that quorum-sensing systems of P. aeruginosa display a complexity even within the same species, and the production of certain AHL signal molecules may be associated with certain phenotypes in P. aeruginosa.