The Ph.D. program in Systems Science (SyS) equips students with advanced skills for tackling research on technological, natural, economic, and social systems using mathematical models. Throughout their doctoral studies, SyS students learn various skills that enable them to create, employ, and implement techniques for analyzing and predicting complex phenomena. These techniques involve analytical, numerical, and computational models that originate from first principles or data, incorporating a range of interdisciplinary fields such as mathematics, operations research, physics, statistics, computer science, and engineering. The program encompasses several subjects such as machine learning, network science, analysis and control of dynamical systems, time-series analysis, statistical physics, complex systems theory, numerical optimization, numerical integration of differential equations, statistics, stochastic processes, agent-based models, specification languages, programming, and software analysis.  Students compose tailored study plans by choosing subjects from a wide portfolio of basic and advanced courses, covering a minimum of 150 lecture hours. SyS students also have the opportunity to spend a study period abroad as visiting fellows.

The Florence-Pisa Doctorate in Philosophy was established through an agreement between the University of Florence and the University of Pisa. It aims to train scholars who, drawing on core competencies in all aspects of philosophical disciplines, will provide original contributions in one or more specific fields

The San Raffaele University, top-ranked among the research universities in Italy, offers a PhD program aimed to provide excellent guidance, support and training to graduate students interested in understanding the molecular processes underlying human diseases and in designing new approaches for their treatment.

The Department, like almost all physics departments in Italy, lives in symbiosis with the most important Italian research organizations (CNR, INFN, INAF, ...). Its activity is also in close connection with the LENS (European Laboratory of Non-Linear Spectroscopy): an infrastructure of excellence, unique in Italy, which is also located on the campus.

A thesis for the Doctor of Philosophy (PhD) by Research in Archaeology must explore human societies of the past using their material remains and must implement the development of archaeology as a scientific discipline. Archaeological methods and theories should be explained using case studies from the continents of Africa, Asia, Australia, Europe, and the Americas. The dissertation should include the latest developments in this field and present theories and practices found in scientific reality concerning the latest archaeological discoveries.

PhD in Economics and Finance This PhD programme is jointly run by the Universities of Trento and the Free University of Bozen-Bolzano.

Advancements in genetics and genomics have spurred the emergence of Precision Medicine, which revolutionizes traditional medical approaches by utilizing vast molecular data for personalized disease diagnosis and treatment. The PhD in National PhD in Systems Medicine aims to equip professionals with interdisciplinary skills in biomedical sciences, preparing them to address precision medicine challenges through technological strategies and multidisciplinary approaches.

The PhD School in Legal Sciences includes the following tracks:

PhD in Advanced-Systems Engineering The purpose of this international PhD programme is to train a new generation of researchers able to carry out independent research in the areas of Advanced-Systems Engineering and give them the opportunity to transfer and exchange knowledge with national and international research centers and industries.

PhD in Sustainable Energy and Technologies With this PhD programme we train young researchers in the field of sustainable use of resources in the production systems of energy, of buildings, in energy final utilisation, in the development of products and in manufacturing.

PhD in Education and Social Sciences This PhD programme addresses the study of education and social sciences in an interdisciplinary context, providing the necessary skills to face research in the theoretical and empirical-experimental field and promoting the development of innovative application practices.

This PhD program aims to create a center for higher education and advanced research at the European level in the field of literary, linguistic, and intercultural studies. It is divided into four curricula, two of which are international. The two international curricula (Germanistics and European Founding Myths in Arts and Literature) are aimed at training qualified scientific-professional figures in the field of French and Germanistics, with specific skills also in Italian culture, whose professional outlets may be found in public and private academic and cultural institutions, top management, publishing, museums, conservatories, and communication sectors in Italy, France and Germany. The third curriculum (Language, literature and philology) aims instead to train qualified figures in several disciplinary fields who are able to use integrated methodologies. Individuals may find future employment in universities, international institutions and public relations systems and transnational communication networks. The curriculum of Linguistics and Oriental Studies provides training in linguistics, preparing scholars for careers primarily within universities or other research centers. The training is congruent with the need for language specialization in language education and L2 teaching. Individuals with this PhD will also have skills useful for consulting and highly responsible positions regarding communication in private companies, public administration and cultural heritage contexts, as well as professional tasks in various cultural industries (i.e. publishing, radio, television, new media) and services.

International PhD in Food Engineering and Biotechnology The purpose of this International PhD programme is to train a new generation of globally renowned researchers to apply approaches of engineering and biotechnology to food processing by giving them the opportunities to transfer and exchange knowledge with national and international research centers and industries.

PhD in Computer Science The main goal of this programme is to train future scientists with a strong professional background who are capable of working in an international and highly competitive environment, such as the Information Technology (IT) sector.

Micro- and nano-electronics is considered an essential technology, as it enables the development and growth of our society. It is explicitly mentioned in the most relevant strategic planning documents of Italy and Europe (eg: PNRR 21-26, European Commission, of which it is one of the Key Enabling Technologies, and the European Chips Act). Today, any technological development, in any sector, from telecommunications to biomedical, from mobility and transportation to energy, requires dedicated micro- and nano-electronic devices, which must be specifically developed and manufactured on large scale. The problem at an international level, identified with the term "chip shortage", which has clearly emerged in recent years, demonstrates how the world economy is increasingly bound to the availability of integrated circuits and systems.

The PhD program in "Mathematics, Computer Science, Statistics", based in Firenze, is managed by a Consortium among the University of Firenze, the University of Perugia and the Istituto Nazionale di Alta Matematica "F. Severi"-Rome (INdAM). This PhD program inherited the tradition of the pre-existing three separate PhD's in Mathematics, Computer Science, Statistics, and can rely upon the very many, and well established, scientific connections of the involved institutions with Universities and Research Centers in many Countries of the World. The relevant number of offered scholarships allows the achievement of a critical mass of PhD students and activities, which are fundamental for a doctorate with an interdisciplinary character.

The PhD in Economics aims to train research doctors who, in addition to possessing a high level of expertise as regards all the fundamental aspects (methodological, theoretical, analytical) of economic science, are also capable of producing original scientific research within their chosen area of specialization for the purpose of producing the doctoral thesis.