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Objective To observe ultramicro pathologic change of rabbit brain central damaged tissue and peripheral tissue after LOT, to evaluate the changed structure of blood brain barrier (BBB) of peripheral tissue in acute stage. Method Seventy Newzealand rabbits were randomly screened from Zhejiang University Animal Experiment Center. By stereotaxic technique, semiconductor surgica laser fibers were inserted into right frontal lobes and heat treated to randomly build LITT Group A (2 W, 600 s, n = 20) and LITT Group B (15 W, 100 s, n = 20) brain damaged models successfully. Other 15 nomal rabbits were randomly distributed as mannitol perfusion group and fake operation group. The ultramicro structures in central thermodamaged tissue were observed with transmission electro microscope after LITT 3 h,6 h,12 h,24 h. In peripheral tissue, ultramicro morphologic changes of brain vessels and BBB were evaluated. S100B protein in serum and BBB indexe were measured at different stages post LITT. Experimental data were treated as one-factor analysis of variance and q test. Results The brain damage center connected the tip of laser fiber and turn into thermodamage tissue. The main structure changes were cytoclasis, damnification of cell membrum, swelling of cell organelle such as mitochondrion, endoplasmic reticulurn,disappearance of mitochondrion and sparseness of cytoplasm in local tissure. Heat energy conducted to damage peripheral tissue, some cells occured apoptosis in different stage. In acute stage after LITT, contracted capillary vessel, oncreted red cell, swell endothelium cell, broken base membrum, wide around clearance and destroyed aperture structure were identified. The levels of serum S100B and BBB indexe dramatically rised. The opening time of BBB in peripheral tissue was longer than mannital perfusion group. However at 24 h post LITT, they began to recover in Group A. The difference of serum S100B and BBB indexe between Group A and Group B has statistical significance ( P =0.0087). Conclusions With semiconductor laser heat treatment and stereotaxic techniqe, definite cells cytoclasis, cell membrance structures and chondriosome damage could be performed obviously in rabbit brain thermotherapy point. Apoptosis could be found in peripheral tissue, BBB could be opened in an acute stage. The opening time course of BBB was shortened in those LITT cases with small power. It shew us a new method to perform a safe and exact damage zone of brain for functional neurosurgery.