This research has the objective to determine the profiles of scientific publications in Muslim countries, including: the position of Muslim countries developing scientific publications through scientific journals; an overview of scientific journals that develop in Muslim countries; and an overview of scientific journals that develop in Muslims countries as an indicator of opportunities and challenges of scientific publications for Islamic Universities in Indonesia. The research method used was content analysis with the main data source from The Islamic World Science Citation Center (ISC). The data analysis used descriptive statistics with percentage model, and it was described in qualitative descriptive. The results demonstrate that the most widely owned scientific publications are from Malaysia, followed by Iran and Pakistan, which is above 100. The scientific publications, over 40 in number, come from Turkey, Saudi Arabia, and Egypt. The scientific publications, at around 14-24 in number, come from India, Jordan, Indonesia, and Azerbaijan. In addition to the 10 countries mentioned above, 20 other countries have approximately 1-7 scientific publications on average. The lack of scientific publications in Muslim countries becomes a great opportunity and challenge for Islamic Universities in Indonesia for producing quality scientific publications.