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Stella Maris College was conferred autonomous status in 1987. Autonomy has given the College the freedom to design syllabi, introduce new programmes and courses, introduce innovative assessment and testing patterns, conduct examinations and announce results. The degrees are given by the University of Madras, with the name of the College on the certificate.

The introduction of the Choice-based Credit system in 1997 further enabled the introduction of contemporary courses that had both national and global relevance. Inter-disciplinary electives and application-orientation subjects, as well as various career oriented projects were introduced in all disciplines. Today, students can choose from a wide range of course options suited to their needs.

The Autonomous status of the college also made possible the introduction of two new and important courses: Value Education and the Social Awareness Programme.