Introduction: Digestion is an important step in urine iodine determination methods. High temperatures and long heating durations can be considered as weaknesses of the present methods. The aim of the study was assessment of microwave use for digestion of urine and decompostion of interfering substances, aimed at shortening the time and increasing safety in the procedure. Materials and Methods: Random urine samples were processed by conventional acid digestion and also by new microwave optimized digestion methods. After digestion, iodine levels of samples, digested by the two mentioned methods, were also determined using chemical colorimetric kinetic reaction Ce+4 and Ce+3 according to the well known Sandell-Kolthoff reaction. Microplate reading format by ELISA reader was used to increase speed and precision of reading. Sensitivity, precision and comparison results were assayed in both the methods as well. Results: Optimized microwave digestion showed that merely a 10 min duration is adequate for complete digestion of urine samples. Intra- and inter- assay coefficients of variation were 6.7- 9.3% and 9.8-12.3% respectively. The final results of the comparison of iodine contents of samples, were obtained through the two microwave and conventional methods, showed acceptable correlation (r=0.928). The assay recovery was 91-113% and the sensitivity 5 µg/dL. Conclusion: The results of this study showed that the microwave procedure for urine digestion is acceptable. The digestion method obtained comparable results with conventional digestion methods, and can hence replace conventional electrical heat digestion methods.