Pseudomonas aeruginosa is a model organism for the study of intercellular communication and biofilm formation. As such, P. aeruginosa has been the subject of several microarray analyses comparing gene expression in biofilms and planktonic cultures. In the current work, we carried out a meta-analysis of these data sets to try and identify genes that are generically associated with biofilm formation in all of the conditions examined. Although the total number of transcripts modulated in the biofilms was large within the individual studies, the overlap between the data sets was small. Indeed, only five transcripts were upregulated and six transcripts were downregulated by more than twofold in the three data sets analysed. However, when the threshold modulation was relaxed to less than twofold, the overlap between the data sets increased, revealing a set of transcripts common to all of the studies. Transcriptional fusions and quantitative real-time PCR were used to independently confirm a selection of the observed modulations. Notably, we found that the expression profile of genes encoding the catabolic pathways for branched chain and aromatic amino acids was altered in biofilms, and that these alterations correlated with the onset of anaerobic growth. These findings were confirmed by quantitative amino acid analysis of culture supernatants. A mutant in one of the genes that we identified showed diminished biofilm formation in an attachment assay. The relatively small number of common biofilm-specific endpoint transcripts throws doubt on the suggestion that biofim formation proceeds through a pre-determined developmental pathway.