The problem of constructing an intelligent system for diagnosing heart valve disease is considered. It is shown that the diagnosis is established on the basis of the results of a standard examination, which includes anamnesis, laboratory data, electrocardiogram, echocardiography and Doppler examination. The use of hybrid neural networks of ensemble topology is substantiated for solving the problem. In order to show that the appropriate neural networks for composing an ensemble can be effectively selected from a set of available neural networks, an algorithm for structural-parametric synthesis of hybrid neural networks of ensemble topology is proposed. As for training component neural networks it is used Bagging approach. Accuracy and diversity were used as criteria. The structure of the diagnostic system for recognition of valvular heart disease is presented. The results of research of the developed software are presented. As for training component neural networks, the Baging approach is used. The structure of the diagnostic system for recognition of valvular heart disease is presented. The results of the study of the developed software are presented.