The first structured doctoral programme in Portugal, the Gulbenkian Doctoral Programme in Biology and Medicine (PGDBM) was launched in 1993, through the collaboration between the Calouste Gulbenkian Foundation, the Secretary of State for Higher Education, the National Board of Scientific and Technological Research and later the Foundation for Science and Technology, which later became associated with the Luso-American Development Foundation. The programme was designed as a limited-time pilot programme, aimed at training one hundred doctors, and lasted seven years.

The PGDB was a natural progression of the PGDBM programme launched in 1993, funded by the Calouste Gulbenkian Foundation (FCG), the Ministries of Education and Science and Technology and the Luso-American Development Foundation (FLAD). As with the PGDBM, the PGDB provided a full year of postgraduate courses and laboratory rotation, followed by three years of guided research work, leading to a doctoral thesis to be presented at a Portuguese or foreign university.

The Doctoral Programme of the Instituto Gulbenkian de Ciência (PDIGC) was launched in 2003. The aim of the PDIGC was to provide a research training environment at the IGC so that PhD students could develop the skills and knowledge to contribute to research as professionals. Unlike PGDBM and PGDB students who did their theses abroad, PDIGC students did their theses in IGC laboratories.

The programme's structure was identical to the PGDBM and PGDB, but now with students from different backgrounds, not only academic, but also cultural, and the collective spirit was now created within the same institute.

PIBS students were selected by an evaluation committee from a large pool of applicants from around the world, and from very diverse backgrounds, not restricted to the life sciences. After 4 months of courses taught by several IGC professors and guest scientists, students had a period for reflection and research project writing together with their chosen supervisors.

The IGC Doctoral Programme allows students to come into contact with a wide range of different topics in biological sciences, promoting independent and critical thinking through various exercises. In the first year, students attend a series of courses, covering both fundamental concepts and cutting-edge research in biology, taught by IGC researchers and visiting professors from prestigious universities and research institutes around the world. The programme also includes courses in partnership with the Champalimaud Foundation and the University of Cologne/Max Planck Institute. At the end of the first semester, students had several weeks to develop a research proposal for their theses, and to find a researcher at the IGC who will supervise their doctoral work.

Four-year programme with the support of Siemens Portugal and FCT, with one year of full-time courses, workshops and projects on the main aspects of computational biology from a biological, computational, mathematical, chemical and physical point of view, and three years of research training in a laboratory recognized around the world, including Portugal.

During its four editions more than 35 highly motivated doctors were recruited. These students were trainees or specialists who, as a complement to their clinical practice, intended to acquire a solid scientific background as a basis for excellence in medical research and clinical practice. Students received six-month postgraduate courses by an international faculty, followed by doctoral thesis work at national or international institutions.

The Champalimaud Doctoral Programme in Neuroscience, created in 2007 by the newly established Champalimaud Foundation (FC), was initiated and hosted at the IGC. Seven editions were still held at the IGC. In 2010, it was transferred to the new Champalimaud Centre for the Unknown, in Lisbon. This programme aimed to train students to carry out innovative and integrative research into the biological basis of behavior.

The PGCD was an innovative programme that prepared students from different PALOP countries and Timor-Leste to pursue a scientific career, particularly in the area of ​​life sciences, making them excellent teachers for the new generations of African and Timorese students.The programme, although inspired by IGC doctoral programmes, had a different basis, recruiting students from Angola, Mozambique, Cape Verde, Guinea-Bissau and S. Tomé and Príncipe, who had classes in Cape Verde, in Portuguese, having taken also English classes. Training a new generation of Portuguese-speaking Timorese and African scientists, giving them the opportunity to study and practice advanced science was the aim of the programme.