Introduction <p>Post-thyroidectomy hypocalcemia remains a common and clinically significant complication. Despite advances in surgical technique and perioperative care, rates of transient and persistent hypocalcemia remain substantial, with reported transient rates up to 50% and persistent rates up to 4%. This study evaluates the impact of intraoperative parathyroid gland identification and accidental removal on postoperative hypocalcemia in a Swiss hospital.</p> Methods <p>We conducted a retrospective analysis of 615 adult patients undergoing thyroid surgery at the University Hospital of Basel between 2007 and 2022. 322 patients (52.3%) who received total thyroidectomy were selected for statistical analysis. Data on demographics, intraoperative nerve monitoring, number of parathyroid glands visually identified, histological confirmation of gland removal and use of autotransplantation were collected. Postoperative hypocalcemia was categorized as temporary (&lt; 6 months) or persistent (&gt; 6 months). Statistical analyses included chi-squared tests, Wilcoxon rank-sum tests, and logistic regression to assess associations between gland identification/removal and hypocalcemia, with significance set at <i>p</i> &lt; 0.05.</p> Results <p>Among 288 patients who underwent total thyroidectomy with intraoperative identification of parathyroid glands, 43% (<i>n</i> = 124) developed temporary hypocalcemia and 0.9% (<i>n</i> = 3) experienced persistent hypocalcemia. Surgeons identified a median of 2.54 parathyroid glands intraoperatively, with no significant association emerging between the number of glands identified and temporary hypocalcemia (<i>p</i> = 0.594). Histological evidence of inadvertent gland removal occurred in 18.6% of cases and correlated with a non-significantly higher rate of temporary hypocalcemia (47.3% vs. 40.5%, <i>p</i> = 0.402). Parathyroid autotransplantation had a significantly higher rate of postoperative hypocalcemia compared with those without autotransplantation (61.0% vs. 38.6%; OR 2.48, 95% CI 1.26–4.87; <i>p</i> = 0.007).</p> Conclusion <p>Our findings suggest that intraoperative visual identification of parathyroid glands alone may not be sufficient to reliably predict postoperative hypocalcemia, highlighting the multifactorial nature of postoperative calcium disturbances. Accidental gland removal increases temporary hypocalcemia but lacks statistical significance. Autotransplantation, while useful for preserving long-term function, may initially exacerbate transient hypocalcemia. Meticulous surgical techniques and preservation of gland vascularity remain paramount to minimize hypocalcemia risk. Future prospective studies should evaluate the role of novel intraoperative identification technologies in reducing these complications.</p>