Pro-angiogenic factors [vascular endothelial growth factor (VEGF) and basic fibroblast growth factor (bFGF)] and anti-angiogenic factors (endostatin) play important roles in the progression of pancreatic cancer. The purpose of the present study was to investigate the knockdown effect by either VEGF or bFGF siRNA on the expression and secretion of endostatin in pancreatic carcinoma cells. Pancreatic carcinoma cell lines (sw1990, Panc-1 and PCT-3) were treated with VEGF and bFGF siRNA. The expression of VEGF, bFGF and endostatin in pancreatic carcinoma cell lines was determined by reverse transcription-polymerase chain reaction (RT-PCR) and western blot analysis. Secretion of endostatin was measured by enzyme-linked immunosorbent assay (ELISA). bFGF and VEGF siRNA significantly reduced the expression of bFGF and VEGF mRNA, respectively, but did not affect mRNA and protein expression of endostatin in pancreatic carcinoma cell lines. However, secretion of endostatin in PCT-3, Panc-1 and sw1990 cells was significantly inhibited by bFGF and VEGF siRNA. This study demonstrated that pro-angiogenic factors (VEGF and bFGF) differentially modulate expression and secretion of anti-angiogenic factors (endostatin). This result may have important implications in the anti-angiogenesis therapy in pancreatic cancer.