Rationale, aims and objectives Baseline thyroid function testing and regular follow-up of thyroid function under amiodarone usage was recommended by guidelines. Little is known about the status of amiodarone monitoring in real-world clinical care in Taiwan. The objective was to determine the rate of thyroid monitoring and to assess the clinical and physicians' characteristics associated with adequate monitoring in a tertiary referral centre for arrhythmia. Methods We reviewed the medical records of patients receiving amiodarone during the period 2008-2009 at Taipei Veterans General Hospital. The rate of baseline and follow-up thyroid function monitoring during amiodarone therapy were calculated. Factors associated with guideline adherence to monitoring were analysed. Results Among the 1319 enrolled cases, 36.4% (n = 480) underwent baseline thyroid function testing and 1.1% (n = 15) received measurement of anti-thyroid peroxidase antibody before amiodarone initiation. Regular follow up of thyroid function under amiodarone usage occurred in only 8.6% (n = 114) of cases. Baseline thyroid function was more likely to be present in patients of younger age (P < 0.001), female sex (P = 0.01), and in those who received amiodarone therapy from cardiologists (P < 0.001) or electrophysiologists (P < 0.001) with fewer years of service (P < 0.001). Upon multivariate analysis, only physicians' expertise (cardiologist versus non-cardiologist, OR = 5.67, 95% CI: 2.44-13.16) and years of service (OR = 0.97, 95% CI: 0.95-0.998) were significantly associated with adequate thyroid monitoring. Conclusions The rate of thyroid monitoring with amiodarone therapy had been suboptimal. Strategies to enhance guideline adherence are needed.