Thulium lasers operating near approximately 2 microm are the subject of interest for various medical applications. The newly developed Tm3+ silica fibre laser in Q-switched and CW operation was investigated to determine its efficiency in the interaction with soft and hard tissues. The interaction was investigated using a free-running continuous (CW) Tm(3+)-doped fibre laser (wavelength 1.99 microm, with self-pulsation ranging over 1 to few tens of microseconds) and for novel Q-switched operation of the same fibre laser (pulse durations from 150 to 900 ns and pulse repetition rates from 100 Hz to 17 kHz). Residual damage and affected zones using the Q-switched laser were nearly six times smaller than using the CW fibre laser for about 50 s of exposure time, and increased with pulse repetition rate. The energy required to ablate tissue with the Q-switched fibre laser ranged from 0.2 to 0.6 kJ/cm3 and was significantly smaller than that for the CW fibre laser of 153 to 334 kJ/cm3. Under both high-resolution reflected optical microscopy and histological examination, tissue crater depths were observed as cleanly cut with smooth walls and minimal charring in the case of Q-switched operation of the fibre laser. This study is the first direct comparison of tissue interaction of short-pulse (Q-switched) and CW Tm(3+)-doped silica fibre lasers on crater depth, heat of ablation and collateral damage. The Q-switched Tm(3+)-doped silica fibre laser effectively ablates tissue with little secondary damage.