Aberystwyth, Bangor and Swansea universities have become independent of the University of Wales from today.
Swansea and Bangor Universities are now independent institutions
Their new status was being greeted as an important milestone although University of Wales degrees will still be awarded.
The changes are part of a modernisation within the university system in Wales.
The University of Wales, founded in 1893, called it a "new era" and a spokeswoman said: "We're all moving forward and modernising our structure."
It is felt that the changes could help the universities' ability to develop and compete for students.
Aberystwyth, Bangor and Cardiff were original founding members of the University of Wales, while Swansea joined in 1920, and it grew to a federation of nine universities and colleges.
Two years ago, Cardiff University dropped out but remains an affiliated institution.
Swansea said it wished to have "a full and mutually beneficial relationship" with a modernised University of Wales and would still be awarding its degrees for "the foreseeable future".
Vice-chancellor Professor Richard B Davies said Swansea had "truly come of age".
The change is seen as helping the universities compete for students
He said: "The formal change in our status is more than a symbolic name change.
"It heralds a bright new era for the university, an era that will see our ambitious plans come to fruition and Swansea University becoming a truly world-class, research-led institution."
He said it will include a revamped corporate image, including a "fresh, modern look" to the traditional university crest.
Owen Morgan, president of Swansea University's Students' Union, said: "Students already know it as Swansea University, however it has taken time to get the name officially changed.
"Will most students notice the change? Yes I think they probably will.
"It is recognition for the students and staff who study and work here."
Dr David Roberts, registrar at the re-named Bangor University, said the decision would not affect the 10,000 students or their degree programmes.
"This is a legal and constitutional change, but it is a significant one in terms of the university's standing, and a very important milestone in our history.
"It shows great confidence in the activities, policies and procedures of the university."
Aberystwyth University has not made any formal statement but is expected to reveal a new corporate image next month.
The developments also reflect major changes at the University of Wales, which will cease to be a federal institution.
A review of its role, functions and structure was held in 2005, chaired by former Plaid Cymru leader Dafydd Wigley.
The university plans to still be accrediting and validating degrees, while also continuing to have a role in research and protecting and promoting the language and culture of Wales.