A method of calibration of a mathematical model for the compensation of errors due to dynamic deformation of a measuring machine equipped with a mobile unit able to move a stylus probe in un measuring volume, wherein the model provides, in response to at least one input quantity correlated with a control signal of said drive means, a plurality of output quantities comprising at least one component of the measurement error introduced by the deformation and at least one quantity detected by a laser sensor and correlated with the deformation. In the calibration step, the mobile unit is subjected to a movement cycle constituted by small-amplitude oscillations of variable frequency, following the law of sinusoidal motion, keeping the tip of the probe blocked; during the movement cycle, the input and output quantities are sampled and supplied to an algorithm for model identification.