Focusing femtosecond (fs) laser pulses into transparent media, such as corneal tissue, leads to optical breakdown, generation of a micro-plasma and, thus, a cutting effect inside the tissue—provided the intensity at the focus exceeds a threshold which depends on the pulse duration. For fs pulses, the corresponding threshold pulse energy is reduced by some orders of magnitude compared with ns or ps pulses. At a low pulse energy, thermal and mechanical damage to surrounding tissue is minimized, enabling a highly precise cutting effect inside the tissue while leaving anterior layers unaltered. In the following, investigations concerning aspects of the interaction of ultrashort laser pulses with aqueous media are presented: in particular, detection of pressure transients and bubble formation. For the first time—to our knowledge—the content of the resulting gas bubbles was analysed by gas chromatography, giving evidence of molecular hydrogen. Secondly, the potential of three-dimensional cutting effects within the corneal stroma for refractive surgery applications was evaluated in vitro on freshly enucleated porcine eyeglobes. Laser pulses with a duration of 200–300 fs and energies of 1.5–600 J were provided by a mode-locked Ti:sapphire laser with subsequent chirped pulse amplification.