Software system quality control of templates is offered and methodology of automation testing of current system is developed. Software systems has a high noise immunity significatives, that provides an opportunity to reduce the requirements to it hardware performance. This allow resolve the contradiction between high cost of control and necessity development of small and medium batches of microelectronic products. Execution of experiments on large amounts of data by manual way has led to an increase in the time that spent on testing the system. Proposed to automate this process. Software complex QuickTest Professional as the automated tool was selected. It allows to developing automatic tests for application, that based on using of various modern technology of developing software products and includes the usable instrument of data parameterization. Using of Data Table object during the developing of automatic script allowed to parameterize of input values for the implementation iterative of data-in. The analysis of test results is executed. The positive estimates of iterations passage is obtained. Applying of automation testing methodology of software system allowed to reduce of testing time in compare with manual method.