The treatment planning system (TPS) has become a key element in the radiotherapy process with the introduction of computer tomography (CT) based 3D conformal treatment planning. Commissioning of a MLC on a TPS either for conformal radiotherapy or intensity modulated radiation therapy (IMRT) requires beam data to be generated on a linear accelerator. Most of the TPS require these beam data to be generated with routine collimator jaws. However some TPS demand the data to be provided for MLC shaped fields. This prompted us to investigate whether beam data with jaws differ than that with MLC and whether the jaw based beam data would suffice for the commissioning of a MLC on a TPS.Beam data like percentage depth dose (PDD), cross beam profiles and output factors was acquired for jaws and MLC defined square fields for 6, 10 and 23 MV photon beams. Percentage depth dose and cross beam profiles were acquired with a radiation field analyzer RFA-200, CC13-S ion chambers with active volume of 0.13 cm3 and OmniPro-Accept software from Scanditronix-Wellhofer. A Medtec-TG51 water tank with Max-4000 electrometer and 0.6 cc PTW ionization chamber and a mini phantom from Standard Imaging was utilized for output measurements for millennium-120 MLC (Varian Medical Systems) and SRS diode detector (Scanditronix-Wellhofer) of 0.6 mm diameter of active area and 0.3 mm of active volume thickness for micro-MLC (BrainLab).The difference in PDD in the build-up region for millennium MLC was ±1.0% for 6 MV photons. For 10 MV photons the PDD difference was within ±4.0%. The difference in PDD for 23 MV photons ranged from 0% to 40.0%. PDD difference from build-up depth to about 28 cm was within ±1.0%. Difference in PDD crossed ±1.0% at 30 cm depth for 6 MV photons. The difference in PDD in the build-up region for mMLC was ±8.0% for 6 MV photons. For the smallest field size studied with micro-MLC i.e. 0.6 × 0.6 cm2 difference in PDD was more than ±1.0% in the build-up region and beyond a depth of 8.0 cm. The profiles for jaws and MLC agreed within the umbra region. However in the penumbra region small differences in doses were observed. The collimator scatter factor (Sc), phantom scatter factor (Sp) and output factor values for MLC were different that those for jaws.The differences in beam characteristics could have implication for intensity modulated radiation therapy and stereotactic radiosurgery in terms of dose in the build up region, exit dose, dose to the planning target volume (PTV) and organ at risk (OAR). Impact of these dosimetric differences between jaw and MLC needs to be further studied in terms of dose volume histograms for PTV and OAR and its further impact on tumor control probability (TCP) and normal tissue complication probability (NTCP).