This publication deals with the application of standards for industrial automation during distributed control systems design. Control systems design consists of a choice between two approaches based on the standards, IEC 61131 and IEC 61499. The question is which of the standards to use for distributed control systems design. The most commonly used standards are briefly listed in the introduction section. Then follows a more detailed description of the IEC 61131 and IEC 61499 standards, future development of the IEC 61499 standard and its usage during the creation of distributed control systems. Further on are lists and descriptions of existing commercial and research software tools, which are necessary in implementing this standard. The main section deals with the methodology for standard application comparison and criteria selection for comparing. This methodology is then verified on real control systems. The final section includes methodology generalization for suitable approach selection, resulting in recommendations for which standard to choose during creation of distributed control systems.