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p-Cresol is a toxic aromatic compound found in the environment and is a constituent of many disinfectants and preservatives. It may act as a tumor promoter and the US Environmental Protection Agency has listed it as a possible human carcinogen. Thauera aromatica strain T1 is a facultative anaerobic, denitrifying, Gram-negative bacterium that is able to degrade many aromatic compounds including toluene and p-cresol. A proteomics approach was used to identify proteins from T. aromatica strain T1 that have differential expression when cells are induced by p-cresol in comparison to benzoate, a common downstream metabolic intermediate in the degradation of many aromatic compounds. Sequences of peptides from proteins selectively up-regulated by p-cresol in comparison to benzoate were obtained by MS analysis and compared against databases of known proteins from other microorganisms. The sequenced peptides from one of the isolated proteins induced by p-cresol matched a hypothetical protein from a different T. aromatica strain and another matched a hypothetical protein from Azoarcus sp. strain EbN1. Using PCR with degenerate oligonucleotides, the gene fragments corresponding to these proteins were obtained from the T1 genome. Expression analysis also showed differential up- regulation at the RNA level for both these genes when compared to cells induced by benzoate. Using the genome sequence of T. aromatica strain 3CB2, the full-length genes corresponding to these proteins have been cloned from the T. aromatica strain T1 genome. The genes are named pipA and pipB (for p-cresol induced protein) and were determined to reside in a cluster within the T. aromatica strain T1 genome. Bioinformatic analyses of the corresponding gene and protein sequences of pipA and pipB show that these proteins are conserved in many bacterial species involved in aromatic compound biodegradation. PipA is predicted to be an outer membrane transport protein and PipB shows significant homology to a chaperone involved in sorting of lipoproteins in the outer membrane of bacteria. We hypothesize that these proteins may be components of bacterial nanopods that are involved in the uptake of a range of aromatic metabolites from the environment by the aromatic compound degrading bacterial species in the soil and the process may be energy-dependent.