Students spend most of their practical training at Motol University Hospital, the clinical base of the Second Faculty of Medicine and one of the largest and most developed hospitals in Central Europe. Motol University Hospital provides care in all the medical fields for residents of Prague and the whole of the Czech Republic. It is famous for its treatment of distinguished VIP patients, including the Czech President. It has a total number of approximately 2 300 beds, of which 690 are in the Paediatric section, while the adult section has 1 230 beds. Annually, over 70 000 patients are admitted to the hospital, and more than 750 000 outpatients are treated. A total of 3 000 medical staff are employed, including 800 medical doctors. All Paediatric departments are highly specialised, with some medical services being unique in the Czech Republic (Oncology, Haemodialysis, Epileptology, etc.).

Students' practical training also takes place at Na Bulovce Hospital and the Military University Hospital Prague.