Waterjet dissection is under close investigation as a new neurosurgical tool. Experimentally, a precise tissue dissection with vessel preservation has been demonstrated in the porcine cadaver brain. The safety of the device has been shown in first clinical applications. However, a detailed in-vivo analysis of the waterjet device is still awaited. In the present study, two often applied nozzle types (100 microm diameter emitting a coherent straight jet; 120 microm diameter emitting a helically rotating jet) were experimentally studied in vivo. Forty-one rabbits received a frontal waterjet corticotomy on either side with one nozzle type after microsurgical removal of the arachnoid membranes. Animals were sacrificed at 1, 3, 7 days and 6 weeks after surgery. Dissection morphology and vessel preservation were evaluated. Tissue trauma was analyzed by the extent of intra-operative haemorrhage, postsurgical oedema formation and astrocytic as well as microglial reactions. In all animals, reliable brain dissection was observed. Macroscopically, only minor bleeding occurred. Microscopically, also very precise brain dissection with both nozzle types was found. Vessels were preserved with both pressures applied (5 and 10 bar). Dissections with the 100 microm straight nozzle were more precise with respect to dissection margins. However, no significant difference in vessel preservation and extent of haemorrhage, oedema formation, astrocytic and microglial reactivity was shown. Malfunction defined as clotting of the instrument occurred only with the 100 microm nozzle. In four 100 microm straight nozzle hemispheres, even no brain dissection was seen. The results indicate that the waterjet enables very precise and reliable brain parenchyma dissection with minimal trauma and vessel preservation in vivo. If this can be proven to be of clinical relevance, the instrument will become a valuable neurosurgical tool. Based on these results, the authors selected the 120 microm Helix nozzle for further research with this device in the CNS.