A system for sterilising pharmaceutical products already packaged in containers, comprising a path (10) for feeding the products packaged in containers, said path (10) comprising:- a chamber (2) for heating the products already packaged in containers- a cooling chamber (3) located downstream of the heating chamber (2) the cooling chamber (3) being separate from the heating chamber (2)- means (4) for regulating the pressure in the heating chamber (2) and/or in the cooling chamber (3) so as to minimise the risk of the containers being deformed as a result of the pressure variation inside the containers, said pressure variation inside the containers being due to the heating/cooling.