We propose a new approach to study the various aspects of the practical application of structural identification algorithms. We analyze the risks arising by applying these algorithms at the pre-design stages of creating automatic control systems. In particular, we show that using these algorithms creates the possibility of an unforeseen deterioration in the estimation quality of a technical object's output variable. We formulate methodological recommendations for the practical application of structural identification algorithms. In particular, we are developing a flowchart for searching for an adequate mathematical model of a technical object based on the use of structural identification algorithms. We present a preliminary assessment of the information capabilities of structural identification algorithms.