A software program [MU-EPID], has been developed to perform patient specific pre-treatment quality assurance (QA) verification for intensity modulated radiation therapy (IMRT) using fluence maps measured with an electronic portal imaging device (EPID). The software converts the EPID acquired images of each IMRT beam, to fluence maps that are equivalent to those calculated by the treatment planning system (TPS). The software has the capability to process Varian, Elekta and Siemens EPID DICOM images. In the present investigation, several IMRT plans for different treatment sites were used to validate the software using the Varian a-Si 1000 EPID with the Pinnacle TPS. A total of 20 IMRT plans of different treatment sites were analyzed. Isodose distributions, dose profiles, dose volume histograms (DVH's) and gamma analysis comparisons were performed to evaluate the accuracy of our method. A gamma index analysis of the isocenter coronal plane was done for each plan and showed an average of 97.44% of gamma passing rate using a 3% and 3 mm gamma criterion. Isodose, DVH and dose profile comparisons were conducted between the original calculated plan and the measured reconstructed plan from the EPID images processed through the MU-EPID software. The results suggest that MU-EPID can be used clinically for patient specific IMRT QA, providing a comprehensive 3D dosimetric evaluation through DVH comparison as well as an option for a 2D gamma analysis.