Ischemic Brain Stroke is considered to be one of the most significant reason causing mortality of patients. During first 60 days after brain stroke some critical symptoms are localized. Eventual registration of physiological parameters or biomedical signals e.g. heart rate variability within that time results in extremely difficult interpretation, most likely at the certain border of commonly understand sense. Therefore proper rehabilitation of such patients associated with well estimated results is very important as significantly decreases their mortality and leaves them in the highest possible well being. Due to rather bad quality of registered signals the need of more sophisticated processing method is necessary. The paper presents application of PDM for decomposition of HRV signals spectrum and separate estimation of behavior of both sympathetic and parasympathetic nervous activity. Simple ANOVA test applied for properly prepared data proved the anticipated results concerning significant difference of certain parameters e.g. sympatho-vagal balance estimated within mentioned 60 days period.