Secularism and Challenges of Contemporary Islamic Thought. Renaissance in the West comes with scientific paradigm that emphasizes the ratio aspect and denies the transcendental aspect. Cartesian Newtonian paradigm resulted in progress to the West to secularistically, materialistically and positivistically, so it’s not unfriendly to the existence of religions. Religion is removed from the public and private spheres. This article examines the history, character and characteristics of Western secularism and its impact on world religions and human beings, especially Islam. This study is focused on the aspects of Western secular scientific paradigm, because behind the scientific aspects of this paradigm is the foundation of civilization. The results of this paper prove that modern Western science offered to non-Western societies is not neutral and full of values. Western science is not value-free (value free), but is full with value (value laden). Therefore,it is expected that the community of non-Western civilizations that is familiar with spiritual values, especially Islam, could be critical and wise in accepting the products of Western civilization, especially the scientific field.