He initially remained in academia, in patient care as an oncohematology physician and conducting research at university hospitals in Saarland and Zürich.

In 2001, while maintaining his position at the University of Mainz, Şahin began to engage in entrepreneurial activities, co-founding two pharmaceutical companies, in 2001 and 2008, with his partner and spouse Özlem Türeci.

As a result of the company's increase in value, Şahin and Türeci became the first Germans with Turkish roots among Germany's 100 wealthiest people.

[10][11][12] Taking advanced courses in mathematics and chemistry, he graduated from the Erich-Kästner-Gymnasium in Cologne-Niehl in 1984, and was the first child at the school with Turkish guest worker parents.

[27] In 2017, Sahin was involved in establishing the new Helmholtz Institute HI-TRON, which is a cooperation between the German Cancer Research Center (DKFZ) and TRON.

TRON is a non-profit (private) biopharmaceutical research institute that develops new diagnostic tools and drugs to treat cancer and other diseases with a high unmet medical need.

[37] Şahin co-founded the company Ganymed Pharmaceuticals in 2001 with his wife Özlem Türeci and his mentor Christoph Huber.

[39] In 2016, after showing in a randomized clinical trial that this drug significantly boosted advanced gastric cancer patients' overall survival,[40] the company was sold to Astellas Pharma for over €400 million.

[42][43][44] Together with Özlem Türeci and Christoph Huber, Şahin founded the biotechnology company BioNTech, based in Mainz, Germany, in 2008 and serves as its CEO.

[49][50] Since April 2020, BioNTech has been researching a vaccine for the disease COVID-19 under Şahin and Türeci, who is also a member of the company's board of directors.

This application offers the possibility of targeting each patient's tumor mutations with an individually tailored mRNA vaccine of unique composition that is produced "on demand".

They observed strong tumor-antigen-specific immune responses induced by their uridine-based non-nucleoside modified mRNA vaccines, even though the utilized TAAs are self-antigens.

This was a critical step toward the development of effective, potent cancer vaccines targeting a broad range of antigens for immunotherapy.

Chimeric antigen receptor (CAR)-T cell therapies (CARVAC) are promising immunotherapies for treating B-cell-derived hematologic cancers.

Sahin and his team have developed ways to use RNA vaccine technology for in vivo expansion and enhanced engraftment of genetically engineered, adoptively transferred CAR-T cells.

Combating autoimmune diseases is challenging and can lead to systemic immunosuppression and side effects such as increased risk of infection.

Şahin and his team developed a novel therapeutic strategy that circumvents systemic immunosuppression by inhibiting only the immune cells that mediate autoimmune disease.

The RNA vaccine used for tolerance induction contained 1-methylpseudouridine (m1Ψ) instead of uridine, a modification previously described by Katalin Karikó and colleagues that does not stimulate Toll-like receptors.

In mouse models of MS, the novel RNA vaccine approach delayed onset and reduced severity of established disease without inducing generalized immunosuppression.

[71][72][63] Clinical trials and subsequent real-world studies established that BNT162b2 vaccine is very effective in inducing immune responses and proved the safety and potent efficacy in humans.