The requirement for higher precision gears is a constant in various manufacturing processes due to the necessity to improve the performance and efficiency of mechanical systems. Cold forming is one of such processes, especially for the manufacture of precision pinions with complex geometries. Misalignments between axes in the forming system (die and nesting assembly) can generate severe errors, mainly when the required dimensional and shape deviations are of some micrometers. In this context, this study investigates the influence of the reference axis on the measurement of geometric and dimensional deviations of dies used in the cold forming process for the manufacturing of spur gears. The die package tool was analyzed, consisting in the Shrink ring, the upper die and the forming die. The ISO 1328-1/2 standard was used to select the specific parameters to describe the gearing quality of the dies and the DIN 3962 standard was used for the quality classification. The evaluation was done by focusing on the isolated deviations: profile, helix, single and total cumulative pitch, and radial runout. The results showed that the choice of reference axis (top die or gear die) significantly influences some measured deviations. For profile and flank line deviations there was no significant difference, while for pitch and radial run-out deviations significant differences were observed. The statistical analysis of variance (ANOVA) confirmed run-out errors higher than 10 µm, presenting significant influence on the measurement results. This study highlights the importance of choosing the reference axis for dimensional measurement of dies with complex geometries, which is crucial to guaranteeing the desired gear quality produced by cold forming.