In this paper, a conceptual multi-zone model for climate control of a live stock building is elaborated. The main challenge of this research is to estimate the parameters of a nonlinear hybrid model. A recursive estimation algorithm, the Extended Kalman Filter (EKF) is implemented for estimation. Since the EKF is sensitive to the initial guess, in the following the estimation process is split up into simple parts and approximate parameters are found with a non recursive least squares method in order to provide good initial values. Results based on experiments from a real life stable facility are presented at the end.