Introduction: This study aimed at answering three research questions: (1) Under the experimental conditions studied, what is the dominant mechanism of Holmium:YAG lithotripsy with or without pulse modulation? (2) Under what circumstances can laser pulse modulation increase crater volume of stone ablation per joule of emitted radiant energy? (3) Are BegoStone phantoms a suitable model for laser lithotripsy studies? Materials and Methods: The research questions were addressed by ablation experiments with BegoStone phantoms and native stones. Experiments were performed under three stone conditions: dry stones in air, hydrated stones in air, and hydrated stones in water. Single pulses with and without pulse modulation were applied. For each pulse mode, temporal profile, transmission through 1 mm water, and cavitation bubble collapse pressures were measured and compared. For each stone condition and pulse mode, stones were ablated with a fiber separation distance of 1 mm and crater volumes were measured using optical coherence tomography. Results: Pulses with and without pulse modulation had high (>80%) transmission through 1 mm of water. Pulses without pulse modulation generated much higher peak pressures than those with pulse modulation (62.3 vs 11.4 bar). Pulse modulation resulted in similar or larger craters than without pulse modulation. Trends in BegoStone crater volumes differed from trends in native stones. Conclusions: This results of this study suggest that the dominant mechanism is photothermal with possible photoacoustic contributions for some stone compositions. Pulse modulation can increase ablation volume per joule of emitted radiant energy, but the effect may be composition specific. BegoStones showed unique infrared ablation characteristics compared with native stones and are not a suitable model for laser lithotripsy studies.