Background Thymokidney has been reported as an approach for a vascularized thymus for transplantation to induce donor specific tolerance.A completely thymectomized model which ensures that the obtained thymus is not injured has not been developed yet and it would be useful for evaluating autologous thymokidney function in rats.Methods Adult Sprague-Dawley male rats weighing 150-300 g (n=30) underwent non-invasive intubation with the assistance of an improved self-made wedge-shaped cannula made from a 2-ml plastic syringe and transillumination from the anterior tracheal area by an operation spotlight.The rats then received a thoracotomy while their breathing was supported by a small animal ventilator,and both lobes of the thymus were entirely extirpated under a 10x microscope.The postoperative survival rate of the rats was recorded,and changes in the T-cell reservoir from 9 of 30 rats within 21 days after surgery were monitored using flow cytometry.The complete thymectomy rate was confirmed by autopsy and histological examination on 21 days post-operation.Results The postoperative survival rate of rats was 100%.The exsected thymus was free of injury and the rate of complete thymectomy was 100%.Conclusions This model has a stable survival rate and complete thymectomy is able to be achieved.The obtained thymus tissue is free of injury and can be used for transplantation.