The response regulatory gene flcA controls the differentiation process of Azospirillum brasilense from vegetative state to cyst-like forms, both in culture and in association with plants. In contrast to the wild type parental strain Sp7, strain Sp72002, a Tn5 induced flcA(-) mutant, does not aggregate, does not differentiate from motile, vibroid cells into nonmotile, cyst-like forms and lacks some of the exopolysaccharide material on its cell surface. Here we aimed to identify differentially expressed genes whose expression could be modulated by flcA. Using cDNA-amplified fragment length polymorphism, we detected 81 transcript-derived fragments showing differential expression during exponential growth phase in an aggregation-inducing medium containing high C : N ratio. The fragments were sequenced and analyzed, and expression of ten genes encoding known proteins was compared between the two strains by reverse transcriptase polymerase chain reaction-(RT-PCR). RT-PCR analyses confirmed the differential patterns observed by cDNA-AFLP in nine of those genes. Among them are genes homologous to nodQ, involved in sulfation; narK, involved in nitrite/nitrate transport, and flp, involved in autoaggregation; as well as genes encoding a biopolymer transport protein, and the signal recognition particle. This work demonstrates the usefulness of the cDNA-AFLP approach to reveal genes that are differentially expressed during aggregation in Azospirillum brasilense and provides insights into the aggregation process of this bacterium.