Background: SNAP-tag, a self-labeling protein tag, is commonly used for in vitro and in vivo analysis of bound target proteins. We report the first evidence that SNAP-tag could be used for ex vivo detection of enriched biological markers. Methods: Proof of concept was established for target c-kit receptor, a pathological and diagnostic marker for a variety of cancers. SNAP-tag conjugates with stem-cell factor (SCF) fusion proteins were designed and their binding and specificity was validated in vitro using flow cytometry and immunostaining. Results: Ex vivo diagnostic application of the fusion protein was demonstrated in comparison with anti-c-kit antibody for peripheral blood samples from leukemia patients and colorectal tissue specimens. © 2017, Springer International Publishing Switzerland.