In radiation therapy, the monitor units (MU) needed to deliver a treatment plan are calculated by treatment planning systems (TPS). The essential part of quality assurance is to verify the MU with independent monitor unit calculation to correct any potential errors prior to the start of treatment. In this study, we have compared the MU calculated by TPS and by independent MU verification software. The MU verification software was commissioned and tested for the data integrity to ensure that the correct beam data was considered for MU calculations. The accuracy of the calculations was tested by creating a series of test plans and comparing them with ion chamber measurements. The results show that there is good agreement between the two. The MU difference (MUdiff) between the monitor unit calculations of TPS and independent MU verification system was calculated for 623 fields from 245 patients and was analyzed by treatment site for head & neck, thorax, breast, abdomen and pelvis. The mean MUdiff of −0.838% with a standard deviation of 3.04% was observed for all 623 fields. The site specific standard deviation of MUdiff was as follows: abdomen and pelvis (<1.75%), head & neck (2.5%), thorax (2.32%) and breast (6.01%). The disparities were analyzed and different correction methods were used to reduce the disparity.