1988
Hans J. Müller-Eberhard (1927-1998) is appointed to reorganize the structure of the institute. A number of new scientific working groups applying molecular biological and immunological methods are installed.

1989
Egbert Tannich shows that Entamoeba histolytica can be differentiated in two morphologically similar, but genetically distinct species.

1990
The institute is renamed the "Bernhard Nocht Institute for Tropical Medicine". Due to the Liberian civil war the research facilities near Bong Town have to be abandoned.

1996
Bernhard Fleischer (*1950) becomes director of the institute. The scientific evaluation by the German Science Council published in 1996 recognizes the positive development of the institute in the past ten years.

1997
The City State of Hamburg and the Republic of Ghana sign a State Agreement to establish the "Kumasi Centre for Collaborative Research in Tropical Medicine" (KCCR), a cooperative research institute jointly organised by BNI and Kwame Nkrumah University of Science and Technology in Kumasi. The opening ceremony is held in Kumasi on February 19th, 1998.

1998
The appointment of Prof. Egbert Tannich as holder of the 3rd Chair in Tropical Medicine of the University of Hamburg marks the fulfilment of the main components of the reorganization of BNI, which began in 1988. Achim Hoerauf identifies the bacterial symbionts of the nematode Onchocerca volvulus as a target for chemotherapy of onchocerciasis (river blindness).

2000
The year marks the 100th anniversary of the institute. The celebrations comprise six international scientific meetings and culminate at a ceremony at the Hamburg town hall in October led by the Mayor of the City State and the German Minister of Health. To celebrate the institute, a special stamp is issued by the German Mail (see also Centenary exhibition (in German with summaries in English). The institute's new Travel Medicine Centre is opened.

2001
On the occasion of an international conference on filariasis, co-organised by the World Health Organization (WHO), which attracted over 100 scientists from 22 countries, the historical Bernhard Nocht Medal is handed to Prof. Eric Ottesen (Atlanta) for his excellent contribution to the control of filarial infections.

2002
The institute is appointed National Reference Centre for tropical-disease pathogens by the Federal Ministry of Health. Designing work of the architects Kister, Scheitauer & Gross of Cologne is selected from 65 proposals for a replacement and extension building of the animal facilities and high-security laboratories of the Institute.

2003
Christian Drosten and Stephan Günther of the Department of Virology, headed Prof. Herbert Schmitz, succeed in identifying, from a case imported into Frankfurt Airport, a coronavirus as the cause for an outbreak of a novel disease termed Severe Adult Respiratory Syndrome (SARS) originating in Southeast Asia and threatening to spread around the world. Importantly, ignoring all opportunities of intellectual property rights, the laboratory details necessary to diagnose the new infection are being publicised in the internet promptly in the night of the discovery. A diagnostic kit developed by the BNI scientists in co-operation with partners of BNI spin-off "artus Ltd" is launched for world-wide distribution a few weeks later.

2005
The German Federal Armed Forces and the Institute sign a contract on a co-operation for services and research in tropical medicine. The Mayor of Hamburg and the German Minister of Health attend a ceremony for laying the foundation stone of the replacement and extension building. The Order of Merit of the Federal Republic of Germany BNI is awarded to BNI pathologists Prof. Paul Racz und Dr. Klara Tenner-Racz for their lifetime achievements in HIV research and to the virologists Dr. Christian Drosten and Dr. Stephan Günther for the discovery of SARS-coronavirus.

2006
The clinical department of the Institute is transferred to the University Hospital Hamburg-Eppendorf (UKE) because introduction of Disease Related Groups (DGR) in Germany resulted in a general shortening of hospital stays, an abundance of hospital beds in the country, a rapid decline in the transfer of patients to BNI and, consequently, vacancies and a budgetary deficit of the clinical department. Volker Heussler´s group discovers "merosomes", a previously unrecognised early blood stage in the life cycle of malaria parasites.

2007
The Kumasi Centre for Collaborative Research in Tropical Medicine in Ghana (KCCR) celebrates its 10th anniversary.


2008
The Institute becomes an independent legal entity, a Foundation under Public Law. At the same time, the political responsibility for the institute was given over from the Department of Health of the Hamburg Government to the Department of Science and Research. BNI now is run by a Board of Directors, nominated for five years by the Board of Trustees [Kuratorium] and designed to include two or three scientists and the chief administrator. The initial board members are Prof. Bernhard Fleischer, Prof. Rolf Horstmann (Chair) and Prof. Egbert Tannich and Udo Gawenda as the chief administrator. The Board of Trustees now comprises three representatives each of the State of Hamburg and the Federal Government as well as the Chairperson of the Scientific Advisory Board, two elected members of the Institute and two external experts representing fields of interest for the development of the Institute. As before it is headed by the Senator of the Hamburg Government department responsible for the institute or his/her representative, usually a Secretary of State [Staatsrat], at present Staatsrat Bernd Reinert.