Blooms of the freshwater cyanobacterium Anabaena circinalis are recognised as an important health risk worldwide due to the production of a range of toxins such as saxitoxin (STX) and its derivatives, also known as paralytic shellfish poisoning (PSP) toxins. In this study the transcriptional profile of PSP toxin-producing and non-toxic strains of A. circinalis was investigated by means of a DNA microarray approach. Additionally, gene expression was studied after exposure of toxic A. circinalis cultures to lidocaine hydrochloride at 1 microM for 2 h. Under standard growth conditions, a limited number of putative toxic-strain distinctive DNA fragments, identified in previous studies, were preferentially expressed in toxic versus non-toxic strains. The same genes did not significantly change their expression after exposure to 1 microM lidocaine, conditions previously shown to induce STX production in the cyanobacterium Cylindrospermopsis raciborskii T3. Lidocaine supplementation, however, enhanced the transcription of genes involved in physiological adaptive responses and bloom formation in cyanobacteria, such as the gas vesicle structural protein A and phycocyanin. The heat shock protein HSP-70 and the chlorophyll-a binding protein isiA were significantly repressed by lidocaine exposure. Stress response proteins and genes implicated in secondary metabolism were repressed, including phosphopantetheinyl transferases. The BGGM1 DNA microarray, used in this study, was shown to be suitable for gene expression studies in cultured toxic cyanobacteria and allowed the analysis of gene transcripts associated with surface scum formation by toxic A. circinalis.