Contemporary functional tomographic neuroimaging methods (fMRI and PET) have for many years been applied actively not only in basic studies of brain functions, but also in clinical practice. This article considers the main characteristics of the signals recorded and the principles of constructing images, as well as the requirements for obtaining adequate results. The advantages and fundamental limitations of contemporary tomographic methods of studying brain functions are discussed. The need to use complex approaches consisting of combined studies in investigating the brain is demonstrated, and methods for studying the functional integration of the brain are proposed.