SummaryThe small intestine is an excellent model for studying changes in vasculature in response to different diseases or gene deletions. Here, we present a protocol for whole-mount immunofluorescence staining of blood and lymphatic vessels in the adult mouse small intestine. We describe the steps for perfusion fixation, tissue sample preparation, immunofluorescence staining, and whole-mount preparation of stained samples. Our protocol will enable researchers to visualize and analyze the intricate network of vessels in the small intestine.For complete details on the use and execution of this protocol, please refer to Karaman et al. (2022).1