Small non-coding RNAs including microRNAs and small interfering RNAs play important roles in many biological processes of many organisms. Argonaute proteins serve as a key component of the RNA-induced silencing complex for mediating miRNA/siRNA functions. In the present study, we systematically investigated Argonaute proteins in Schistosoma japonicum by using bioinformatics in combination with 5'- and 3'-Rapid Amplification of cDNA ends techniques and thus obtained three full-length cDNAs encoding Argonaute proteins, named as SjAgo1, SjAgo2, and SjAgo3, respectively. Additionally, SjAgo1/2/3 were differentially expressed in different developmental stages of schistosomes as determined by real-time RT-PCR and Western blot. Taken together, our preliminary results suggested that SjAgo1/2/3 may control gene expression during the life cycle of S. japonicum and therefore may regulate schistosome development and other biological processes.