Aims and background: The Bethesda system for reporting thyroid cytopathology (BSRTC) was introduced to standardize reporting and improve clinical management of thyroid nodules. In general, BSRTC has been reported to have a good diagnostic relationship with the final histopathology (HP) result. This study was aimed at evaluating the malignancy rates of BSRTC at our center, Hospital Putrajaya in Malaysia. Materials and methods: This was a retrospective study of 854 patients who had undergone fine needle aspiration cytology (FNAC) of the thyroid gland nodules at Hospital Putrajaya, which is one of the main endocrine surgery centers in Malaysia from 2008 to 2017. The FNAC results were compared with the final HP results if surgical excision was done, and malignancy rates were calculated. Results: A total of 990 patients with thyroid nodules underwent FNAC at our center during the study period; however, only 854 patients had complete records (729 female and 125 male). A total of 439 patients underwent surgical excision, therefore bearing final HP. Malignancy rates of each BSRTC category were 33.3% in the nondiagnostic/unsatisfactory (ND/US) category, 8.5% within the benign category, 23.2% within the atypia of undetermined significance/follicular lesion of undetermined significance (AUS/FLUS) category, 66.7% in the follicular neoplasm/suspicious of follicular neoplasm (FN/SFN) category, 75% within the suspicious for malignancy (SM) category, and 100% in the malignant category. Conclusion: In our cohort, malignancy rates were higher than the ideal rate suggested by the revised BSRTC guidelines. Strong clinical judgment is required in interpreting FNAC results when using the BSRTC. More data is required to improve the utility of the BSRTC.