The growth disorder influences craniofacial development and early loss of permanent teeth. This case reports the importance of computerized tomography (CT) and surgical guide to identify horizontal bone loss, adjacent teeth and to guide drills when placing implants in a short stature patient. The patient has idiopathic short stature and the 3rd grade of intellectual disability. To recover posterior mandibular teeth, implant treatment was planned. CT images showed that the adjacent teeth were located markedly to the buccal side. A CT-based surgical guide was fabricated and implants was placed using flapless surgery. Bone dehiscence and fenestration may happen when the surgical guide was fabricated just based on adjacent clinical crowns. Thus, it is essential to analysis bone and teeth and to make surgical guide through CT, especially in atrophied bone on grow disorder patients. Furthermore, systematic researches are recommended to elucidate the relationship between growth disorder and tooth malposition.