We identified the proteins secreted by A. flavus and A. fumigatus conidia during the early stages of growth. A comparative analysis was done between the exoproteome of the two species to identify the core proteins that were common between the two Aspergilli as well as species specific signature protiens. The common proteins included cell wall polysaccharide modifying enzymes and those required for nutrient acquisition. The core proteome is an indication that A. flavus and A. fumigatus share the common events during germination and growth. On the other hand, each Aspergillus had a unique subset of proteins that could be potential virulence factors or effector molecules. This species-specific exoprotein signature probably reflects the specific requirements of the Aspergillus pathogen to establish an infection in a particular niche.