The proteome is defined as a group of entire proteins encoded by the genome and the secretome is a subset of the proteome secreted from the cell via several well-studied systems including type III secretion system in bacteria. Recent days, it is proved that secreted proteins of malaria parasites and Oomycetes, once-classified-in-fungi, which infect and modulate the human and plants host cells have conserved additional motif such as RXLR. In the fungal kingdom which has abundant genomes of pathogenic organisms, however, there is no systematic approach for manipulating secretomes. Here we developed the FSD (Fungal Secretome Database; http://fsd.snu.ac.kr/) for collecting and analyzing fungal secretomes of 61 species from the data warehouse of the CFGP (Comparative Fungal Genomics Platform; http://cfgp.snu.ac.kr/) with SignalP 3.0. In the FSD, 107,859 putative proteins which have signal peptides and 10,230 putative signal anchor proteins are archived from our filtering engine with following criteria: 1) the position of cleavage site should occur in the first 70 amino acids from the N-terminal, 2) and the HMM scores and NN scores, in case of signal peptides, should be greater than 0.93 and 0.65, respectively. The ratio of predicted results to total ORFs in Magnaporthe oryzae is 10.12%, which is significantly high ratio compared with 4.62%, the average. The FSD will provide the standardized platform for studying fungal secretome with user-friendly web interface.