Knowledge of a machine tool axis to axis geometric location errors allows compensation and corrective actions to be taken to enhance its volumetric accuracy. Several procedures exist, involving either lengthy individual test for each geometric error or faster single tests to identify all errors at once. This study focuses on the closed kinematic chain method which uses a single setup test to identify the eight link errors of a five axis machine tool. The identification is based on volumetric error measurements for different poses with a non-contact Cartesian measuring instrument called CapBall, developed in house. In order to evaluate the uncertainty on each identified error, a multi-output Monte Carlo approach is implemented. Uncertainty sources in the measurement and identification chain such as sensors output, machine drift and frame transformation uncertainties can be included in the model and propagated to the identified errors. The estimated uncertainties are finally compared to experimental results to assess the method. It also reveals that the effect of the drift, a disturbance, must be simulated as a function of time in the Monte Carlo approach. Results shows that the machine drift is an important uncertainty source for the machine tested.