The program for the Master's Degree in Science, with specialty in Optics, started in September, 1984, while the program for the PhD Degree in Science, with specialty in Optics, started in 1987. In 1993, the program for Direct Doctorate was started, which had the characteristic of not having as a prior requirement the possession of the Degree of Master in Science, meaning that while this program was operational, the Master's program was not implemented at the Center. During all this time, and up to August, 2000, all the certificates corresponding to the Master's and PhD programs were issued by the University of Guanajuato through an agreement with CIO.

After the registration of the Graduate Studies programs before the Ministry of Education (Secretaría de Educación Pública, SEP), by virtue of the recognition of official validity of studies, CIO opted to issue the corresponding certificates through agreements number 2014106 and 2015107, respectively.

As of August, 2003, CIO directly registers the programs for the Master's and PhD Degrees with specialty in Optics before the General Direction of Professions, based on quarterly school terms; this procedure is done so on the grounds of CIO having been recognized as a Public Research Center.

The graduate studies programs are developed by the researchers at the Center, which has always given such programs great quality, and upon the development of CONACYT's Register of Graduate Programs of Excellence, in 1991, our programs were recognized as programs of excellence; later, in 2001, they were recognized as being Top Level.

Since CONACYT implemented these programs, and having CIO achieved the aforementioned recognitions, every student who is accepted into our graduate studies programs, is directly granted a scholarship from CONACYT.