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Introduction: Postoperative hypocalcemia is the most common complication of thyroidectomy. Incidental parathyroidectomy (IP) was thought to be associated with postoperative hypocalcemia. However, according to previous studies, the risk factors and clinical outcomes of IP remain controversial. Methods: Eligible studies were searched in databases including PubMed, Web of Science, and EMBASE from January 1990 to September 2017. Articles focusing on the relationship between IP and postoperative hypocalcemia were included. The risk of publication bias was assessed using Begg’s test and Egger’s regression asymmetry test. Pooled analysis was performed to evaluate the effect of IP on postoperative hypocalcemia and related risk factors. Sensitivity analysis was also conducted to test the stability of our results. The effects of hypocalcemia type, permanent definition, IP incidence, total thyroidectomy, and malignancy operation were also examined using a further subgroup analysis. Results: Thirty-five studies were finally included in the analysis after an exhaustive literature review. Pathology data demonstrate that incidental parathyroidectomy occurred in various locations: intrathyroidal (2.2–50.0%), intracapsular (16.7–40.0%) and extracapsular (15.7–81.1%) regions. Overall, the analysis found that malignancy (RR = 1.60, 95% CI: 1.27 to 2.02; p< 0.0001), central neck dissection (RR = 2.35, 95% CI: 1.47 to 3.75; p = 0.0004), total thyroidectomy (RR = 1.42, 95% CI: 1.20 to 1.67; p< 0.0001) and reoperation (RR = 1.81, 95% CI: 1.20 to 2.75; p = 0.005) were significant risk factors of IP in thyroid surgery. There was an obvious effect of IP on temporary/permanent (RR = 1.59, 95% CI: 1.37 to 1.84; p< 0.0001) and permanent (RD = 0.0220, 95% CI: 0.0069 to 0.0370; p = 0.0042) postoperative hypocalcemia. Sensitivity analysis showed that these results were robust. The subgroup analysis found that IP played a significant role in both biochemical and clinical hypocalcemia in thyroidectomy (p < 0.0001 and p = 0.0003, separately). The association of IP and permanent hypocalcemia using different definitions (6 months or more than 12 months) was also confirmed by the analysis. IP increased the incidence of temporary/permanent and permanent hypocalcemia for cases undergoing total thyroidectomy (40.4% vs 24.8% and 5.8% vs 1.4%, respectively). Thyroidectomy with IP was associated with more permanent hypocalcemia (RR = 3.10, 95% CI: 2.01 to 4.78; p< 0.0001) in malignant cases but was not associated with temporary/permanent hypocalcemia. Conclusions: Malignancy, central neck dissection, total thyroidectomy and reoperation were found to be significant risk factors of IP. IP increases the risk of postoperative hypocalcemia after thyroidectomy. We recommend a more meticulous intraoperative identification of parathyroid gland in thyroidectomy to reduce IP, particularly for total thyroidectomy and malignancy cases. [ABSTRACT FROM AUTHOR]