This paper deals with micro milling cutting process focusing the attention on tool run-out measurement. In fact, among the effects of the scale reduction from macro to micro (i.e., size effects) tool run-out plays an important role. This research is aimed at developing an easy and reliable method to measure tool run-out in micro milling based on experimental tests and an analytical model. From an Industry 4.0 perspective this measuring strategy can be integrated into an adaptive system for controlling cutting forces, with the objective of improving the production quality, the process stability, reducing at the same time the tool wear and the machining costs. The proposed procedure estimates the tool run-out parameters from the tool diameter, the channel width, and the phase angle between the cutting edges. The cutting edge phase measurement is based on the force signal analysis. The developed procedure has been tested on data coming from micro milling experimental tests performed on a Ti6Al4V sample. The results showed that the developed procedure can be successfully used for tool run-out estimation.