Femtosecond lasers start to be routinely used in refractive eye surgery. Current research focuses on their application to glaucoma and cataract surgery as well as cornea transplant procedures. To avoid unwanted tissue damage during the surgical intervention it is of utmost importance to maintain a working energy just above the ablation threshold and maintain the laser energy at this working point independently of the local and global tissue properties. To quantify the attenuation of the laser power density in the tissue by absorption, scattering and modification of the point spread function we monitor the second harmonic radiation generated in the collagen matrix of the cornea when exposed to ultrashort laser pulses. We use a CPA system with a regenerative amplifier delivering pulses at a wavelength of 1.06 µm, pulse durations of 400 fs and a maximum energy of 60 µJ. The repetition rate is adjustable from single shot up to 10 kHz. The experiments are performed on human corneas provided by the French Eye bank. To capture the SHG radiation we use a photomultiplier tube connected to a lockin amplifier tuned to the laser repetition rate. The measured data indicates an exponential decay of the laser beam intensity in the volume of the sample and allows for the quantification of the attenuation coefficient and its correlation with the optical properties of the cornea. Complementary analyses were performed on the samples by ultrastructural histology.