Introduction: Different systems for serum total triiodothyronine (TT3) and total thyroxine (TT4) measuring are performed in clinical laboratories with evaluated consistency. Method comparison and bias estimation are important components of this study. The operation and analytical methods are conducted according to the Clinical and Laboratory Standard Institute (CLSI) new guideline EP09-A3. Methods: The two measurands were analyzed and evaluated on the Roche Cobas e602 and Sysmex HISCL 5000 analyzers. Analytical performance and method comparisons were performed according to EP09-A3. Outliers were computed by statistical methods and classified regression techniques were performed to evaluate and interpret biases. Results: No outliers were detected in this study. Linearity assessment demonstrated a coefficient of correlation as greater than 0.95 for the analytes. The comparison study and 95%CI computed by different regression methods showed acceptable biases except for the weighted Deming regression for TT4 measurement. Conclusion: The study demonstrated excellent analytical performance and acceptable biases for the two systems measuring TT3 and TT4. The new EP09 guide is suitable for the evaluation of methods comparison.