He became the Head of Pharma, Research and Early Development, and a member of the Corporate Executive Committee, of the Swiss healthcare company Roche in 2022.

[17][18] His term concluded in 2015, and he started another lab at the Princess Máxima Center [nl],[8] focusing on childhood cancer,[10] and became the Director Research and Chief Scientific Officer there until 2019.

[7] In 2022, Clevers joined the Swiss healthcare company Roche as its Head of Pharma, Research and Early Development and a member of its Corporate Executive Committee.

[34] His group identified the TCF1 protein, a member of the TCF gene family and a crucial downstream component of the Wnt signaling pathway, making it central in immune responses, embryonic development and tissue repair.

[35] His interest in the gastrointestinal tract began with the discovery that another TCF family member, the TCF4 protein, is required in forming intestinal crypts.

In 2007, Clevers's group identified a marker for stem cells of the small and large intestines, LGR5, itself also a target of the Wnt signaling pathway.

[47] His current major research interest is in using organoids derived from adult stem cells to study the molecular mechanism of tissue and cancer development.