This paper describes a diagnostic protocol of nonlinear dynamic characteristics of biological system using chaos theory. An integrated chaos analysis system for the diagnosis of biological system was designed. We suggest a procedure of attractor reconstruction for reliable qualitative and quantitative analysis. The effect of autonomic nervous system activity on heart rate variability with power spectral analysis and its characteristics of chaotic attractors are investigated. The results show the applicability to evaluate the mental and physical conditions using nonlinear characteristics of biological signal.