Colloid cysts are uncommon benign lesions. There is a lack of consensus regarding the preferred surgical strategy for colloid cyst resection; the technique with the optimal rates of remission, recurrence, mortality, and complications is debatable.To determine surgical outcomes, we performed a systematic review of the published literature on Colloid cysts. Eligible studies (n = 63) with a prospective or retrospective evaluation of endoscopic or microscopic resection of third ventricle colloid cysts were included, which contained data describing extents of resection, seizures, meningitis, and tumor recurrence. A total of 3143 patients (1741 microscopically and 1402 endoscopically operated) were included in the final analysis.According to the results of the meta-analysis, there was a higher rate of gross total resection (GTR) (98.15% versus 91.29%, p = 0.00), need for shunting (4.75% versus 1.46%, p = 0.04), postoperative complications (20.68% versus 10.42%, P = 0.03), mean operating time (194.18 versus 113.04 min), and duration of hospitalization (7.85 versus 4.69 days) for microscopic resection compared with endoscopic resection. While endoscopic resection is associated with a higher rate of cyst recurrence (1.78% versus 0.00%, P = 0.00), there was no difference in reoperation rate (0.49% for endoscopic versus 0.09% for microscopic resection).Microsurgical resection of third ventricle colloid cysts was associated with a higher rate of GTR and a lower rate of recurrence, while there was a lower rate of postoperative complications, duration of surgery, and shorter hospitalization period in the endoscopic group.