Nowadays, femtosecond lasers are routinely used in refractive eye surgery. Until recently, commercialised clinical systems were exclusively based on ytterbium or neodymium-doped solid state lasers emitting sub-picosecond pulses at a wavelength of about 1 µm and repetition rates of a few 10 kHz. These systems use pulse energies in the µJ range and focussing optics of NA = 0.3 to 0.5. Recent developments have provided a variety of alternative and equally viable approaches: systems are now available using nJ pulses at high numerical apertures and MHz repetition rates - an approach so far only used for femtosecond cell surgery - and fibre laser technology is now being used for femtosecond laser corneal surgery. Recent research has also provided more insight in side effects occurring in present systems: self focusing phenomena and so far unexplained periodical structures have been observed even at high numerical apertures (NA >> 0.5) and moderate pulse energies. The interaction of femtosecond laser pulses with strongly scattering tissue has been studied in view of extending the application of femtosecond lasers to keratoplasty for opaque corneas and to glaucoma surgery. The use of new laser wavelengths and adaptive optics has been proposed. Despite the reputation of femtosecond surgical systems for their precision, repeatability and the absence of secondary effects or complications, a closer examination reveals the presence of subtle phenomena which merit further investigation. We present three of these phenomena: the influence of optical aberration on the quality of the incision, the occurrence of filamentation effects, and the deposit of microscopic glass fragments when performing penetrating incisions.