Background: Laser induced protein denaturation is of fundamental interest for understanding the mechanisms of laser tissue interaction. Conjugates of nanoabsorbers coupled to proteins are presented as a model system for investigating ultrafast protein denaturation. Irradiation of the conjugates using repetitive picosecond laser pulses, which are only absorbed by the nanoabsorbers, could result in effects with a spatial confinement of less than 100 nm. Materials and Methods: Experiments were done with bovine intestinal alkaline phosphates (aP) coupled to 15 nm colloidal gold. This complex was irradiated at 527 nm wavelength and 35 ps pulse width with a varying number of pulses ranging form one up to 104. The radiant exposure per pulse was varied form 2 mJ/cm2 to 50 mJ/cm2. Denaturation was detected as a loss of protein function with the help of the fluorescence substrate 4MUP. Results and discussion: Irradiation did result in a steady decrease of the aP activity with increasing radiant exposures and increasing number of pulses. A maximal inactivation of 80% was reached with 104 pulses and 50 mJ/cm2 per pulse. The temperature in the particles and the surrounding water was calculated using Mie's formulas for the absorption of the nanometer gold particles and ana analytical solution of the equations for heat diffusion. With 50 mJ/cm2, the particles are heated above the melting point of gold. Since the temperature calculations strongly depend on changes in the state of matter of the particles and water, a very sophisticated thermal model is necessary to calculate exact temperatures. It is difficult to identify one of the possible mechanisms, thermal denaturation, photochemical denaturation or formation of micro bubbles from the dependance of the inactivation on pulse energy and number of applied pulses. Therefore, experiments are needed to further elucidate the damage mechanisms. In conclusion, denaturing proteins irreversibly via nanoabsorbers using picosecond laser pulses is possible. The confinement of the heat to the nanoabsorbers when irradiating with picosecond pulses suggests that the denaturation of proteins could be possible with nanometer precision in cells with this approach. However, the mechanism of protein inactivation, which is part of present investigations, is crucial for the precision of such nanoeffects.