This study compares the two biggest Islamic organizations in Indonesia, Nahdlatul Ulama(NU) and Muhammadiyah. As previous studies focus on their theological and ideological aspects, this study tries to analyze not only their religious orientation but also position of religious leaders, organizational structure, leadership system, routine activities and susceptibility to new religious change. The second part of this paper deals with religious and socio-political backgrounds under which the two organizations were established and with differences in the ways of interpreting Islamic teachings. This will provide the basis for understanding the dynamics of their later development. The third part explores religious authority supported by both. For this, perspectives on established religious schools, rational interpretation of the Scriptures, mystical practices and hereditary succession of religious leadership are to be analyzed. In addition, the ways different attitudes towards religious authority have impacted on organizational structure are to be examined. The topic of the fourth part is leadership composition, and blood and teacher-student relationships among chairpersons are to be analyzed. The last part deals with how different orientations of the two have impacted on their activities and especially on the ways of accommodating new religious ideas. For this, the ways 'liberal Islamic thought' has been introduced, accommodated and negotiated in each organization are to be compared with. With these discussions, it is expected that religious orientations, organizational structure, leadership system and organizational flexibility of the two can be understood. This analysis can help to have a glimpse on Islamic development in Indonesia and of socio-cultural and political influences the two have exerted on Indonesian society.