This paper presents an analysis of the geometric errors of joint assembly that affect the end-effector for a six-axis industrial robot. The errors were composed of 30 parameters that come from the Geometric Dimensioning and Tolerancing (GD&T) design, which is not the normal way to describe them. Three types of manufacturing tolerancing—perpendicularity, parallelism and position—were introduced and investigated. These errors were measured by the laser tracker. The measurement data were calculated with an analysis of the circle fitting method. The kinematic model and error model based on a combination of translations methods were used. The experiment was carried out in order to calculate the tolerancing of geometric error. Then, the positions of the end-effector in the actual measurement from laser tracker and exact performance were compared. The discrepancy was compensated by offline programming. As a result, the position errors were reduced by 90%.