[en] Large thermal-hydraulic system codes are widely used to perform safety and licensing analyses of nuclear power plants to optimize operational procedures and the plant design itself. Evaluation of the capabilities of these codes are accomplished by comparing the code predictions with the measured experimental data obtained from various types of separate effects and integral test facilities. In recent years, some attempts have been made to establish methodologies to evaluate the accuracy and the uncertainty of the code predictions and consequently judgement on the acceptability of the codes. In none of the methodologies has the influence of the code user on the calculated results been directly addressed. In this paper, the results of the investigations on the user effects for the thermal-hydraulic transient system codes is presented and discussed on the basis of some case studies. The general findings of the investigations show that in addition to user effects, there are other reasons that affect the results of the calculations and which are hidden under user effects. Both the hidden factors and the direct user effects are discussed in detail and general recommendations and conclusions are presented to control and limit them