The list might not be complete.

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
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