The internet-based softwares SignalP v3.0, TargetP v1.01, big-PI predictor and TMHMM v2.0 were combined to predict the signal peptides and the signal peptide-dependent secreted proteins from the 19855 ORFs in Caenorthaditis elegans ws123 genome. 1990 proteins were predicted to be secreted and to contain signal peptides among 19855 proteins, among which 1936 have SignalPaseⅠsignal peptide(containing 41 with RR-motif signal peptide), 53 have SignalPaseⅡ signal peptide and one has SignalPase Ⅳ signal peptide. The signal peptides of 742 secreted proteins include only H-domain and C-domain, but no typical N-domain; the signal peptides of other 1248 secreted proteins include all three domains. Although the amino acids constitution of the SignalPaseⅠsignal peptides were similar in general between Caenorthaditis elegans and prokaryote, there were apparently small differences, and the amino acid composition of Caenorthaditis elegans are more diverse and less conserved. But there are distinct differences on the amino acid composition of SignalPaseⅡ signal peptides. The signal peptides of Caenorthaditis elegans were more diverse than unicellular eukaryotic organism. The signal peptides of a few proteins were exactly the same. We used the BLAST 2 SEQUENECES aligning method to compare the homology among the secreted proteins with the same signal peptides. The alignment results indicated that the genes sharing the same signal peptide sequences were homologous to each other and were likely to have arisen from gene duplication.