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Genetic programming algorithms and other population-based methods are a convenient tool for solving complex interdisciplinary problems. Their characteristic feature is that they flexibly adapt to the problem and expectations of a designer. In this paper they are used for designing complex control systems. In particular a new approach for automatic designing of PID-based controllers which are resistant to noises in the measuring path is proposed. It is based on the knowledge about an object model and capabilities of the genetic algorithm and genetic programming. Not only do these make it possible to tune parameters and select the structure of PID-based controllers, but to also tune parameters of some additional components of a complex controller structure, like parameters of finite impulse response (FIR) filters. The idea of the proposed approach relies on proper encoding of the controller and a dedicated way of evolutionary processing of encoded solutions. The approach proposed in this paper has been tested using a typical control problem, ie a DC motor control problem.