Background In this study, we aimed to compare the accuracy of frozen section evaluation in partial and total laryngectomies performed to treat laryngeal squamous cell carcinoma . Methods A retrospective study was conducted to evaluate the efficacy and accuracy of frozen section analysis for laryngeal squamous cell carcinoma of 65 patients, operated at a tertiary hospital. Two groups were recruited according to the surgical procedure. Results The sensitivity and specificity of frozen section diagnosis in laryngeal cancer were 20% and 99.73%, respectively. For partial laryngectomy, the sensitivity was 16.66% and specificity was 100%. For total laryngectomy, sensitivity was 22.2% and specificity 99.13%. Discordances between the initial frozen section diagnosis and the subsequent permanent section diagnosis were found in 13 (3.35%) pairs (3.37% partial laryngectomy and 3.33% total laryngectomy). Conclusion Our study shows that the surgical method applied has no effect on discordances. However, sampling errors are likely to be more common in partial laryngectomy procedures. It should be kept in mind that the sensitivity of frozen section evaluation is low.