In the article the statistical characteristics of computer model of hypothalamus suprahiazmatic nuclei system and connected with them brain’s structures model are discussed. The equations of weight coefficients algorithm tuning, determined nonlinear function form, incoming in simulation system are listed. Estimations of expected value and variance of error signal, appearing at the tuning model weight coefficients, are discussed. It is shown, that on the value of error signal influence three factors: presence in modeling system the connected brain’s structures, type of teaching signal and dependence the activities frequency of basic pacemaker (hypothalamus suprahiazmatic nuclei) from values photoperiodic rhythm. In the article derivation of theoretical formula of correlation function of output signal of hypothalamus suprahiazmatic nuclei system and form this correlation function, obtaining in computer simulation, are listed. It is shown, that the statistical characteristics proposed model determined the all brain’s structure, including in the system.