Objective: In-vitro investigation of Ho:YAG-laser induced stone fragmentation was performed to identify potential impacts of different pulse durations on stone fragmentation characteristics. Materials and Methods: An innovative Ho:YAG laser system (Swiss LaserClast, EMS S.A., Nyon, Switzerland) with selectable long- or short pulse mode was tested with regard to its fragmentation properties. The pulse duration depends on the specific laser parameter used. Fragmentation tests (hand held, hands free, single pulse induced crater) on artificial BEGO-Stones and fiber burn back tests were performed under reproducible experimental conditions. Additionally, the repulsion of long versus short laser pulses was compared using the pendulum set-up. Results: Differences in fragmentation rates between the two pulse duration regimes were seen. The difference was, however, not statistically significant. Using long pulse mode, the fiber burn back is nearly negligible while in short pulse mode an increased burn back was seen. The results of the pendulum test showed that the deviation induced by the momentum of shorter pulses is increased compared to longer pulses. Conclusion: Long pulse-mode showed reduced side effects like repulsion and fiber burn back in comparison to short pulse-mode while fragmentation rates remained at a comparable level. Lower push back and reduced burn back of longer laser pulses may results in better clinical outcome of laser lithotripsy and more convenient handling during clinical use.