The contemporary medicine heads towards the minimally-invasive diagnosis and treatment methods. Laser-assisted lithotripsy is a minimally-invasive method for destroying or disruption of human urinary stones. The basic principle is the delivery of laser light to the place of urinary stones followed by the absorprion of laser radiation by the urinary stones material which resulted in ablation or plasma vaporization, and finished by fragmentation of urinary stones and spontaneous draining. For the purpose of minimally-invasive laser light delivery the optical fibres or sealed and flexible hollow waveguides are used. In this study we have compared the ablation effect of Ho:YAG laser (with the generated wavelength 2100 nm) and Er:YAG laser (with the generated wavelength 2940 nm) on the artificial samples (special compressed plaster) and human urinary stones in vitro. The reason for the investigating of Er:YAG laser radiation is the fact that the generated wavelength 2940 nm matches the local absorption of water and therefore it is potentially applicable in various medical branches. Both lasers operated in pulsed free-running regime. The Ho:YAG laser was clinically used laser system with low-OH fibre delivery. The Er:YAG laser was laboratory laser system and for the radiation delivery the special COP/Ag hollow glass waveguide sealed with fused silica cap. The ablation or perforation rates were measured and compared for both laser systems, various pulse energy levels and various interaction samples thickness. The interaction environment was water with temperature 25°C. Finally both lasers were tested for human urinary stones lithotripsy in vitro.