In order to investigate the effects of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) on the proliferation, apoptosis of pancreatic cancer cell line SW1990 cells and the expression of cyclin E mRNA, the SW1990 cells were treated with different concentrations of EPA or DHA (20, 40, 60 microg/mL) for 0, 12, 24, 36 and 48 h respectively. By using MTT method, the inhibitory effects of EPA or DHA on the cell growth were assayed. Real time PCR was used to detect the expression changes of cyclin E mRNA after the SW1990 cells were treated with 40 microg/mL EPA or DHA for different time. Flow cytometry was used to test the changes of apoptostic rate in the SW1990 cells treated with different concentrations of EPA or DHA for 24 h. The results showed that EPA and DHA could inhibit the growth of SW1990 cells in a time-and concentration-dependent manner (P<0.01). EPA or DHA could also significantly inhibit the expression of cyclin E mRNA in a time-dependent manner (P<0.05). EPA or DHA could induce the apoptosis of SW1990 cells in a concentration-dependent manner (P<0.01). It was concluded that omega-3 fatty acid could inhibit the proliferation of pancreatic cancer cell line SW1990 cells and promote their apoptosis. The down-regulation of the cyclin E expression by omega-3 fatty acid might be one of the mechanisms for its anti-tumor effect on pancreatic cancer.