The aim of this study is to estimate the relative displacement between the spindle nose and the clamping vice in a rotary transfer machine due to temperature variations. The study was focused on the relative displacements caused by temperature variations produced by two heat sources: the environment around the machine and the three-axis computer numerical control station during the duty cycle. Regarding the last point, an analytical model was developed, in order to account for different thermal sources inside the three-axis module (e.g., ball-screws, rolling bearings, and guideways friction heat, as well as heat generation in the motor). The complete numerical model was calibrated and successfully validated. A comparison was run between numerical results and experimental data in the framework of trials involving a newly developed transfer machine. Finally, the complete model, considering the combination of both the heat sources, has made it possible to estimate spindle nose-clamp relative displacement during a typical working day, highlighting that the radial displacement risks affecting seriously the accuracy of a workpiece.