During infection (in vivo), the entomopathogenic fungus Beauveria bassiana produces yeast-like cells that are surrounded by modified cell walls. These modifications have been related to the fungus ability to limit recognition by the host defense system. The composition of the in vivo cell wall was analyzed using a combination of cytochemical and molecular techniques. The in vivo cell walls still contained both chitin and 1,3-beta-glucan, but they were significantly thinner than in vitro cell walls (50-60 nm versus 100-160 nm, respectively). The difference in cell wall thickness was correlated with transcriptional regulation of cell wall-related genes: quantitative RT-PCR reactions demonstrated that B. bassiana chitin synthase (CHS) and glucan synthase (FKS) genes are down regulated in vivo. These analyses indicate that in vivo-triggered phenotypic modifications, including cell wall adjustments, are controlled by molecular mechanisms that include regulation of gene expression at the transcriptional level.