Aims To compare the safety and efficacy of a new dilator method vs the traditional needle method for transseptal puncture (TSP) in a large cohort study. Methods and results From February 1995 to December 2010, 4443 consecutive patients undergoing TSP done either by a needle method or by a new dilator method were reviewed retrospectively. Data as procedure-related time and complications were evaluated. For the standard needle method, TSP was performed by extending out the needle. In comparison, for the new dilator technique, TSP was performed without an outer sheath and with the needle kept within the dilator; the blunt tip of the dilator was used to help locating the position of the fossa ovalis on purpose. Transseptal puncture was performed by the new dilator method in 2151 patients (48.4%) and by the traditional needle method in 2292 patients (51.6%). The average TSP time needed by the dilator method was longer than that needed by the needle method (5.6 +/- 3.9 vs. 3.8 +/- 2.9 min, P < 0.05). Additional left atrial angiography was required in seven (0.33%) patients for the dilator and in 39 patients (1.70%) for the needle method (P < 0.05). The total rate of severe complications and obvious TSP-related complications was significantly lower in patients who underwent the dilator method than in those who underwent the needle method (0.33 vs. 1.18%, and 0.20 vs. 1.00%, respectively, P < 0.05). Conclusion Our data suggest that the new dilator technique is much safer than that of the standard needle method. It needs relatively longer procedure time but results in significantly fewer episodes of severe complications. Particularly, the blunt tip of the dilator can be used to help locate the fossa ovalis. Therefore, the new dilator technique might be a better choice for relatively less-experienced operators.