For the purpose of biophotonics, free running and Q-switched Er:YAG lasers were constructed. As Q-switches the rotating mirror and Pockels cell were used. In the case of rotating mirror placed inside the resonator the maximum of generated laser energy was 210 mJ in a free-running mode regime when pulses up to 110 μs long (FWHM) were
generated. The resulted parameters of the giant pulses were 30 mJ energy, and 250 ns pulse length. For the Pockels cell Q-switching, the laser was generating 325 mJ of energy in a 250 μs pulse, and 60 mJ of energy in a 60 ns pulse in the case of free running and Q-switched regime, respectively. This output properties together with the generating wavelength (2.94 μm), coinciding exactly with the absorption peak of water, giving us the possibility of using this radiation to the efficient interaction with biological tissue. The transport of the radiation to the interaction place was solved by the special cyclic olefin polymer coated silver hollow glass waveguides with the inner diameter of 700 μm and the length of 10 - 50 cm. For the contact treatment the sealed caps were used for preventing delivery system damage. The aim of this work was except of special laser systems development, the investigation ofthe effect differences between long (free running) and short (nanosecond) laser pulses on ophthalmic (cornea, sclera), urologic (ureter wall), or dental (enamel, dentine) tissue.