Pesticide residues are monitored in many countries around the world. The main aims of the programs are to provide data for dietary exposure assessment of consumers to pesticide residues and for verifying the compliance of the residue concentrations in food with the national or international maximum residue limits. Accurate residue data are required to reach valid conclusions in both cases. The validity of the analytical results can be achieved by the implementation of suitable quality control protocols during sampling and determination of pesticide residues. To enable the evaluation of the reliability of the results, it is not sufficient to test and report the recovery, linearity of calibration, the limit of detection/quantification, and MS detection conditions. The analysts should also pay attention to and possibly report the selection of the portion of sample material extracted and the residue components according to the purpose of the work, quality of calibration, accuracy of standard solutions, and reproducibility of the entire laboratory phase of the determination of pesticide residues. The sources of errors potentially affecting the measured residue values and the methods for controlling them are considered in this article.