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In this study the commissioning of a dose calculation algorithm in a currently used treatment planning system was performed and the calculation accuracy of two available methods in the treatment planning system i.e., collapsed cone convolution (CCC) and equivalent tissue air ratio (ETAR) was verified in tissue heterogeneities. For this purpose an inhomogeneous phantom (IMRT thorax phantom) was used and dose curves obtained by the TPS (treatment planning system) were compared with experimental measurements and Monte Carlo (MCNP code) simulation. Dose measurements were performed by using EDR2 radiographic films within the phantom. Dose difference (DD) between experimental results and two calculation methods was obtained. Results indicate maximum difference of 12% in the lung and 3% in the bone tissue of the phantom between two methods and the CCC algorithm shows more accurate depth dose curves in tissue heterogeneities. Simulation results show the accurate dose estimation by MCNP4C in soft tissue region of the phantom and also better results than ETAR method in bone and lung tissues. [ABSTRACT FROM AUTHOR]