In nature, plants can recognize potential pathogens, thus activating intricate networks of defense signals and reactions. Inducible defense is often mediated by the detection of microbe or pathogen associated molecular pattern elicitors, such as flagellin and chitin. Chitosan, the deacetylated form of chitin, plays a role in inducing protection against pathogens in many plant species. We evaluated the ability of chitosan to confer resistance to Botrytis cinerea in Arabidopsis leaves. We subsequently treated Arabidopsis seedlings with chitosan and carried out a transcript profiling analysis using both ATH1 GeneChip microarrays and quantitative RT-PCR. The results showed that defense response genes, including camalexin biosynthesis genes, were up-regulated by chitosan, both in wild-type and in the chitin-insensitive cerk1 mutant, indicating that chitosan is perceived through a CERK1-independent pathway.