The article presents history of the National Institute of Hygiene (PZH) in the period from September 1939 until the fall of Warsaw Uprising (1944). German occupation left unaltered activities, structure and Polish personnel of the Institute, enforcing commissoner board by professor Ernst Nauck, and subsequently--professor Robert Kudicke from Frankfurt. German production of vaccine against typhus exanthematous for German army was managed by German physician--Herman Wohlrab. National Institute of Hygiene was to be a place modelled on Institute for Tropical Diseases in Hamburg. Polish personnel was subject to military regime, however Feliks Przesmycki, PhD started underground production of vaccine against typhus exanthematous for Polish citizens, which was distributed to prisons (Pawiak Prison) and ghetto. Hospital personnel in Warsaw was also vaccinated. Underground studies programme, including editing handbooks, was set up for the students of closed Microbiology Faculty of Warsaw University, and other wartime conspiracy actions were taken. Personnel of National Institute of Hygiene (PZH) protected research equipment and supplies from war plundering, and supported Polish civilians by e.g. reporting about harmfulness of low-quality and polluted food for the Polish, which Germans supplied market with. During Warsaw Uprising Personnel helped the injured and protected the premises of National Institute of Hygiene (PZH) from burning down; mobile army surgical hospital and pharmacy for the participans of Warsaw Uprising functioned within PZH.