The list might not be complete.

http://www.humboldt-foundation.de
The foundation runs “incoming” and “outgoing” funding programs for postdocs, junior group leaders, and senior scientists. more
http://www.krupp-stiftung.de
The foundation runs several funding programs e.g., for university professors or students. more
http://www.boehringer-ingelheim-stiftung.de/leitbild-und-ziele.html
The foundation offers funding for junior group leaders (medicine, biology or chemistry) already funded e.g., by the Emmy Noether program of the DFG, who need an additional period of up to three years until they are fully eligible for professorship. Applicants active in biology or chemistry can ask for 200,000 to 300,000 Euros per year to complete their research programs. Junior group leaders active in medicine can alternatively ask for funding for a Chair for up to five years. more
http://www.brupbacher-foundation.org/index.php/stiftung
The foundation funds basic oncological research in general. more
http://www.cnv-stiftung.de/de/vorhaben.html
The Foundation for the promotion of science and research, initiated in 2004, supports talented young women with children, thus enabling them to create the freedom and mobility required to further their scientific careers. The Foundation wishes to help prevent science from loosing excellent talent. It is aimed specifically at graduate students in the fields of experimental natural sciences and medicine. more
http://www.daad.de
The German Academic Exchange Service (DAAD) runs mobility programs for students, researchers, graduates, and artists, addressing both German and Non-German citizens. more
http://www.daimler-benz-stiftung.de/cms/index.php
Each year, the foundation awards ten two-year fellowships to postdocs, junior professors or junior research group leaders, endowed with a sum of 20,000 Euros per year. The money can be spent on salaries for scientific assistants, on equipment, research journeys or on attendance fees. Eligible are applicants from any field of research who are somehow linked to a German university or research institution and running (or planning to run) their own research projects. Applicants should be 35 years or younger at the time the fellowship starts. more
http://www.dfg.de
The German Research Association supports researchers at every level of their scientific careers, both with individual funding and in DFG-funded programs, e.g., graduate schools or Clusters of Excellence. more
http://www.dmykg.de
The foundation awards prizes for the promotion of science, for the best poster presentation and for research, and a fellowship to researchers from the German-speaking area who are interested in mycology in human or veterinary medicine. more
http://www.henkel.de/karriere/stipendium-35559.htm
The foundation offers funding for PhD students at private and public universities as well as for postgraduate students planning additional and/or postdoc studies or internships abroad. In principle, the program is open to students from all fields of research, but the focus is on economics, social sciences, natural sciences, and engineering. more
http://www.ekfs.de/de/start.html
The foundation supports mainly clinical medical research, biomedical research, and medical-humanitarian projects. There are several fellowships available for physicians and natural scientists. Besides, universities can apply for funding of Chairs. more
The European Molecular Biology Organization awards fellowships (pre- and postdoc) to life scientists. Junior researchers about to start their own group can apply for a Young Investigators Award, scientists who want to move their labs to one of the EMBO member states can apply for an Installation Grant. In addition to that, EMBO offers funding for the organization of meetings, conferences, symposia, workshops, lecture series, and practical courses, as well as plenary lectures. It is also possible to apply for lecture grants and travel grants. Moreover, EMBO awards the FEBS | EMBO Women in Science Award to a female scientist who has contributed extraordinarily to the field of molecular biology and is a role model for younger female scientists. more
http://erc.europa.eu/
THE ERC supports junior scientists with ERC Starting Grants and senior scientists with ERC Advanced Grants. more
http://www.berg-stiftung.de/
The foundation supports medical science and research. Applications can only be handed in in response to an open call. more
http://fonds.vci.de/
The foundation awards fellowships to students enrolled to become teachers, to PhD students, and to junior professors active in the areas of chemistry. Universities and research organizations can apply for funding for research, teaching, and conferences related to chemistry and adjacent areas. more
http://www.fonte-stiftung.de/
The foundation supports individuals who have already earned their university degrees. Applicants from the humanities can apply for funding for long-term research projects (e.g., doctoral theses, “Habilitation” theses, etc.) as well as for short-term projects (e.g., colloquia, research travels) and for the covering of printing costs or the like. more
http://www.fritz-thyssen-stiftung.de/
The foundation supports
- fixed-term research projects
- junior scientists (postdoc level) with fellowships
- small-scale scientific conferences
- to a limited extent, the publication of research results obtained in funded projects
Applications can only be handed in by researchers already working for a university or a non-profit research organization in Germany or abroad. more
http://www.gerda-henkel-stiftung.de/
The foundation supports fixed-term research projects in the humanities carried out at universities and research institutions. The focus is on postdocs in historical humanities, in science history and historical sub-disciplines, both in Germany and abroad. more
https://www.gdch.de/gdch/preise-und-auszeichnungen/stiftungen.html
There are several foundations that the German Chemists’ Society holds on trust. All foundations award prizes, funding, and/or fellowships to researchers active in chemistry and adjacent areas. more
http://www.hector-stiftung.de/index2.php?seite=hector-stiftung1&sub=1&cat=komplett
The foundation supports medical research, especially in the areas of cancer and HIV/AIDS research. Calls for projects and prizes are published on an annually rotating basis. Calls are published in the first half of each year in the „Deutsches Ärzteblatt“ (miscellaneous) and, for HIV/AIDS research, in addition in the journal „Infektionsepidemiologische Forschung“, published by the Robert Koch Institute. more
http://www.ghst.de
The foundation runs its own projects and funds projects of others, provided that they can be classified as projects concerning “preschool and school”, “academy”, “neuroscience” or “family and profession”.
http://www.hfsp.org/
The Human Frontier Science Programme funds novel, innovative, and interdisciplinary research approaches regarding the complex mechanisms of living organisms, ranging from molecular and cell biology to systemic and cognitive neurosciences and the interactions between different organisms. A special focus is on new collaborations between biologists and researchers from fields such as physics, mathematics, chemistry, computer sciences, and engineering, focusing on research on the frontiers of the life sciences. more
http://www.klinz-stiftung.de/
The foundation supports solely scientists who have earned their PhD / doctoral degree and are holding a non-permanent position. They can apply for funding for materials to use in human and adult stem cell research under an open call. more
http://www.klaus-tschira-stiftung.de/
The foundation supports the natural sciences, mathematics and informatics. Funding will only be awarded to scientific and non-profit institutions. Individuals are not eligible for funding. more
http://www.leopoldina.org/de/foerderung/das-leopoldina-foerderprogramm/
The program is based on four pillars: - the Leopoldina Postdoc Fellowship - a follow-up funding phase after the fellowship has run out - the returning fellow scholarship and - a mentoring program Each year, about 20 postdoc fellowships will be awarded to researchers from Germany, Austria, and Switzerland, who have already earned their PhDs, are active in the natural sciences or in medical research, and have already developed their own research profiles. more
http://www.becker-stiftung.de/
Each year, the foundation awards a prize to junior scientists (any field) who are active in research regarding the physical, mental or cognitive performance and, finally, the maintenance of the working abilities of ageing employees. more
http://www.maxweberstiftung.de/foerderung.html
The Max Weber Foundation is the largest research organization in the humanities. The Max Weber Institutes are located solely outside Germany. Each year, about 110 fellowships are awarded to PhD / doctoral students and postdocs. more
http://www.novartis.de/forschung_entwicklung/stiftung_fuer_therap_forschung/aktivitaeten.shtml
The foundation supports research projects in medicine and adjacent areas carried out at German universities and similar institutions that are characterized by an innovative approach and a specific therapeutic relevance. Besides, the foundation runs a fellowship program for junior scientists. more
http://www.bosch-stiftung.de
The foundation runs several fellowship programs for young managers and young leaders in science. Most of them address graduates and postgraduates from the US and Europe. The two-year program “Fast Track” addresses female postdocs pursuing a career “in academia” and aims at teaching them the necessary skills to plan their careers strategically. There is a call each year, addressing different scientific fields in turn. more
http://www.schram-stiftung.de/foerderprogramm/index.html
The foundation awards funding for brain research projects. more
http://www.studienstiftung.de/stipendienprogramme.html
The foundation supports undergraduate and PhD students, junior scientists, junior journalists and artists. Nominations and self-applications are possible. more
http://www.sdw.org
The foundation supports undergraduate and graduate students. more
http://www.volkswagenstiftung.de
The foundation supports sciences and engineering, both in practical research and teaching. It aims to support research projects dealing with promising topics and to support institutions to optimize their working conditions. A special focus is given to junior researchers and the cooperation of researchers across borders between different disciplines and/or states. more
http://www.kalkhof-rose-stiftung.de/stiftung.html
The foundation supports scientists who have almost finished their „Habilitation“ theses (approx. one year prior to finishing) with fellowships and, in exceptional cases, also by covering expenses for materials or printing. more
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