The Institute was founded in 1918/19, shortly after the reestablishment of Poland as an independent country. It was based on three pre-existing laboratories affiliated with the Scientific Society of Warsaw (Towarzystwo Naukowe Warszawskie): Laboratory of Neurobiology (in existence since 1911), Laboratory of Physiology (in existence since 1913) and Laboratory of General Biology (established in 1918). Formation and development of the Institute was supported in part by a donation of Nadine Sieber-Shumova, a close co-worker of Marceli Nencki from Berne and St. Petersburg.

Over the next two decades the Institute grew to become the leading biological research centre in Poland. The outbreak of World War II interrupted a period of its intensive expansion and achievement of scientific excellence in the field of experimental biology. After the turmoil of World War II, during which over a dozen of the Institute’s staff lost their lives, and its premises (including most of its 30,000-volume library) were destroyed, the surviving staff members (professors Jan Dembowski, Jerzy Konorski, and Włodzimierz Niemierko) re-established the Nencki Institute. In 1952 the Institute was incorporated into the newly founded Polish Academy of Sciences, and the Institute’s director, Prof. Dembowski, became the first President of the Academy. During the period of 1953-55, a newlly erected building at 3 Pasteur Street in Warsaw became the new, and up-to-date, the final home of the Nencki Institute.

In 1990 the Institute was invited to become a member institution of the Global Network for Molecular and Cell Biology (MCBN) within UNESCO. Continuously hiring new talented researchers and awarding approximately 15 doctoral degrees annually, the Nencki Institute is known for its competitiveness in securing external funding for research projects, as well as for the number and quality of its scientific publications.