The purpose of this study was to investigate the changes in the corneal endothelial layer by specular microscopy after surgery in patients with horizontal and oblique strabismus. Eighty-three eyes of 56 patients were evaluated prospectively. There were three subgroups: one horizontal muscle surgery, two horizontal muscle surgery and inferior oblique muscle surgery. Patients were aged 13.58 ±10.39 years (range 4-46) overall: 14.59 ±12.37 in group 1, 12.23 ±7.33 in group 2 and 11.48 ±11.48 in group 3. There were 26 males and 30 females with 22 esotropia, 21 exotropia and 13 inferior oblique overaction. Group 1 included 51 eyes, group 2, 16 eyes and group 3, 16 eyes. Average angle was 33.03 ±13.75PD preoperative and 8.03 ±6.42PD postoperative. Average endothelial cell density values were 3054.12 ±315.30 pre and 3044.44 ±295.78 post; not significantly different. Hexagonality values changed significantly: 53.75 ±9.4 pre to 52.42 ±8.29 post. Chronic stress and time are required for the reduction of endothelial cells. The authors suggest that remodulation or compensation in the vessels after strabismus surgery can eliminate stress in the short-term preventing permanent decrease in endothelial cell density. Strabismus surgery did not affect endothelial cell density in this study. However, hexagonality decreased gradually postoperatively for horizontal muscle surgery but not inferior oblique surgery. This may reflect the role of the anterior ciliary arteries. Changes were temporary.