It is under the conditions of religious tolerance and avoiding prejudices that different thoughts and sometimes the opposite ones could be appeared and accordingly, context of scientific and cultural efflorescence could be created. Tolerance is the factor of dynamism, development and growth of different thoughts and enhances the admission capacity and tolerance of different ideas of the societies subjected to conflicting ideas. Religious tolerance has a significant role in development of science, culture, and scientific and cultural centers and consequently, conditions of scholars in two Alebouyeh and Seljuk periods. Having a contrastive and comparative approach, the present paper analyzes, compares and evaluates religious tolerance in scientific and cultural affairs during two Alebouyeh and Seljuks periods.