We compared urinary calculus fragmentation with long pulsed Ho:YAG (λ= 2.12 μm) versus Er:YAG (λ = 2.94 μm) lasers. We measured the ablation width, depth, volume and efficiency as a function of pulse energy from calculus threshold energy to clinical energy typically used for Ho:YAG laser lithotripsy. Ablation effects were evaluated for three types of urinary calculi (calcium oxalate monohydrate, cystine, and uric acid), for single and multiple pulses applied at various optical energy levels. By means of comparing laser-induced crater topography and ablation volume for each stone type, the feasibility of Er:YAG laser lithotripsy was appraised. The Er:YAG laser pulse energy generated deeper and narrower crater shapes with relatively smooth contours whereas the Ho:YAG laser produced shallower and wider craters with irregular shapes. In terms of multiple pulses ablation, the Er:YAG produced larger ablation volume than Ho:YAG. The deeper crater induced by the Er:YAG was attributed to the higher absorption coefficient of stones at the 2.94 μm wavelength, and widening of crater by Ho:YAG was perhaps caused by lateral expansion of ablated material. Comparing the ablation efficiency, Er:YAG was superior to Ho:YAG for both single and five-pulses.