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Our objective was to investigate the risk of coronary heart disease (CHD) in patients with Hashimoto's thyroiditis (HT).The Taiwan National Health Insurance Research Database was used to conduct a retrospective cohort analysis. The cohort study consisted of 1165 newly diagnosed HT patients and 4660 matched controls (non-HT patients) from 2000 to 2010. The median follow-up time was 5.46 years. The risk of developing CHD for HT patients was measured using the Cox proportional hazards model.The risk of developing CHD in HT patients was increased compared with the non-HT controls, with an adjusted hazard ratio (HR) of 1.44 (95% confidence interval [CI] = 1.05–1.99). The risk was significant in women but not in men, and restricted to subjects younger than 49 years. HT remained an independent risk factor after adjusting for comorbidities; however, combining with hypertension or hyperlipidemia further increased the risk of CHD (adjusted HR = 2.06, 95% CI = 1.46–2.92; and adjusted HR = 1.83, 95% CI = 1.31–2.55, respectively). Furthermore, HT without T4 treatment and HT with treatment for less than 1 year were associated with higher risk of CHD (adjusted HR = 1.55, 95% CI = 0.98–2.46; and adjusted HR = 2.42, 95% CI = 1.43–3.97, respectively). The risk of CHD decreased after treatment with T4 for more than 1 year and did not differ from the non-HT cohort (adjusted HR = 0.84, 95% CI = 0.0.47–1.52).Patients with HT, are at higher risk of developing CHD compared with the general population. Treatment with T4 reduces the risk of CHD.