Objective: We planned to compare the outcome of the standard dissection tonsillectomy and microdebrider intracapsular tonsillectomy on the same patient to avoid confounders that may mask an actual association or, falsely establish an apparent association between the type of surgery and outcome when no actual association between them exists. Patients and Methods: Thirty children with chronic tonsillitis, snoring and sleep apnea due to tonsillar hypertrophy were included in the study. One tonsil was removed using the microdebrider intracpsular method and the other side by the standard dissection technique. The two sides were compared for duration of surgery, intraoperative blood loss, need for bipolar cauterization and stitches, reactionary and secondary bleeding, pain, wound healing and recurrence. Results: The operative time was significantly shorter in tonsillar sides performed with the microdebrider (P-value = 0.02). The intraoperative bleeding and the need for using bipolar diathermy were more in microdebrider (P-value < 0.001 and 0.03, respectively). While the use of stitches was significantly higher with dissection technique (P-value = 0.03). There was no difference regarding postoperative pain in the first day, but subsequently there was more pain among dissection side with significant difference (P-value < 0.001). Healing was significantly faster in microdebrider side (P-value < 0.001). Recurrence was detected among one side operated with the microdebrider with no significant difference between both sides (P-value = 0.3). Conclusion: Microdebrider intracapsular tonsillectomy is a safe and effective procedure in treating children with chronic tonsillitis and sleep apnea.