Er:YAG laser (wavelength 2.94 μm) operating both in free-running and Q-switched regime was designed and developed for the purpose of ureter wall perforation or incision, and urinary stones fragmentation. Component of this system was a special transfer part consisted of a cyclic olefin polymer-coated silver (COP/Ag) hollow glass waveguide (inner/outer diameter 700/850 μm or 320/450 μm) with a sealed cap for a contact treatment. Maximum pulse interaction energy and length for free-running Er:YAG laser were 100 mJ and 200 μs, respectively (corresponding intensity was 130 kW/cm2 for the 700 μm waveguide and 500 kW/cm2 for the 320 μm waveguide). Maximum interaction pulse energy and length in Q-switched regime were 30 mJ and 70 ns, respectively (corresponding intensity was 111 MW/cm2 for the 700 μm waveguide and 357 MW/cm2 for the 320 μm waveguide). Basic interaction characteristics and parameters of ureter wall perforation and urinary stones fragmentation were found. For that reason the number of pulses needed for the perforation of the ureter wall tissue (thickness ∼ 1 mm), ablation threshold and ablation rate were measured for free-running and Q-switched Er:YAG laser radiation. Subsequently, the investigated tissue samples were histologically evaluated after the interaction. The ablation rate of the Q-switched Er:YAG laser radiation was higher compared to the free-running radiation. The application of Q-switched Er:YAG laser radiation on ureter tissue resulted in minimum tissue alteration (up to 50 μm from the surface) without any influence on the deeper layers. The possibility of urinary stones perforation with free-running Er:YAG laser radiation (with maximum interaction energy) was also demonstrated.