This work reports a method based on correlation functions to convert EPID transit signals into in vivo dose values at the isocenter point, Diso, of dynamic IMRT beams supplied by Varian linac. Dose reconstruction for intensity-modulated beams required significant corrections of EPID response, due to the X-ray component transmitted through multileaf collimator. The algorithm was formulated using a set of simulated IMRT beams. The beams were parameterized by means of a fluence inhomogeneity index, FI, introduced to describe the degree of beam modulation with respect to open beams. This way, all dosimetric parameters involved in Diso reconstruction algorithm, such as the correlation functions, the correction factor for EPID to phantom distance and the modulated tissue maximum ratios, were determined as a function of the FI index. Clinical IMRT beams were used to irradiate a homogeneous phantom, and for each beam, the agreement between the reconstructed dose, Diso, and the dose computed by TPS, Diso,TPS, was well within 5 %. Moreover, the average ratios, R, between the Diso, and Diso,TPS, resulted equal to 1.002 ± 0.030. Thirty-five IMRT fields of 5 different patients undergoing radiotherapy for head–neck tumors were tested and the results were displayed on a computer screen after 2 min from the end of the treatment. However, 350 in vivo tests supplied an average ratio R equal to 1.004 ± 0.040. The in vivo dosimetry procedure here presented is among the objectives of a National Project financially supported by the Istituto Nazionale di Fisica Nucleare for the development of in vivo dosimetry procedures (Piermattei et al. in Nucl Instrum Methods Phys Res B 274:42–50, 2012) connected to the Record–Verify system of the radiotherapy center.