The ascomycete fungus Fusarium graminearum is a well-known pathogen of wheat, barley and maize, and it is responsible for devastating diseases Fusarium head blight of wheat and barley, Gibberella stalk rot of maize. Using the strain AmCyanPH-1, which constitutively expresses AmCyan fluorescent protein without affecting fungal growth, we tracked F. graminearum growth inside host plants during disease development, and found the fungus first grows intercellularly. Using laser microdissection, we profiled in planta fungal gene expression during wheat seedling coleoptile infection and during maize stalk infection in a stage-specific manner, and started to understand its molecular strategies in confronting the host environments. Meanwhile, also using laser microdissection, we profiled host cell gene expression in a cell-type and stage-specific manner during maize stalk rot development, and we are in the process to understand host responses to F. graminearum.