We report on laser safety aspects for near infrared femtosecond laser refractive surgery. In particular, the transmittance of microjoule laser pulses at 1040nm through the cornea during flap procedures based on femtosecond laser induced multiphoton ionization and photodisruption has been determined. When using focusing optics with numerical aperture of 0.3, more than 20% of the incident NIR photons are propagating towards the retina. In addition, self-focusing, white light and second harmonic generation, and destructive photodisruptive side effects have to be considered when using such high energy laser pulses of amplified laser systems. Microjoule femtosecond laser pulses in combination with low NA objectives have the potential to induce destructive intraocular side effects. Further studies are required to evaluate the damage potential of the transmitted photons absorbed by the retinal pigment epithelium and other intraocular compartments. Because of the fact that flaps can be also generated with low nanojoule energy femtosecond laser pulses of non-amplified MHz lasers in combination with high NA objectives, compromise between procedure time, pulse energy and numerical apertures has to be found for safe ocular femtosecond laser surgery. Transfection with femtosecond laser pulses is covered by our patents: DE 10223992 A1 DE 10223921 PCT/DE03/01708 CN 1653185 A1 DE 10162176 A1.