In this report we evaluated the effect of femtosecond laser energy on the development of corneal haze and keratocyte activation in rabbits following intra-stromal photodisruption to create LASIK flaps using a modified commercial femtosecond surgical laser. Three groups of flap parameters were studied: 1.5 microJ/pulse with 10 microm spot separation and complete side cut (Group 1); 3.5 microJ/pulse with 14 microm spot separation and complete side cut (Group 2); 3.5 microJ/pulse with 14 microm spot separation and partial (50 microm) side cut (Group 3). All flaps were left attached without lifting to avoid epithelial contamination. Rabbits were then evaluated pre- and post-operatively by quantitative in vivo and ex vivo confocal microscopy. The achieved flap thickness 1 week after surgery averaged 88.9+/-12.8, 90.8+/-6.9 and 86.5+/-6.8 microm for Groups 1-3 respectively (p=NS). Interface thickness was significantly greater (p<0.05) in the higher energy groups averaging 40.0+/-11.2 and 37.7+/-5.7 microm for Groups 2-3 compared to 28.6+/-4.5 microm for Group 1. Corneal haze was barely detectible and not significantly different between groups, although haze was detected in the region of the side-cuts in Groups 1 and 2. No clinically significant changes in stromal or epithelial thickness were noted. Laser confocal microscopy showed the presence of small diameter cells within the flap interface that resided within disrupted regions of the corneal collagen lamellae. Keratocyte activation was only detected in regions of the 100% side cut and not over the flap interface. In conclusion, the results of this study indicate that photodisruption of the corneal stroma alone without flap elevation regardless of laser energy does not induce significant corneal haze in the rabbit. However, a thicker stromal interface was seen with the higher energy suggesting greater stromal damage.