Antibody-targeted vaccination aims to efficiently deliver antigen to dendritic cells by targeting specific receptors at the cell surface. The choice of receptor depends on different factors, including their capacity to induce internalization of the delivered antigen/adjuvant cargo. Assays currently used to monitor internalization in dendritic cells have several limitations. We have developed a novel DNA-based probe that allows for simple and robust high-throughput analysis of internalization. Designed for flow cytometry, the probe can also be used for fluorescence microscopy to clearly distinguish internalized from surface-bound material. Here, we describe the steps for modifying material (antibodies, proteins) with the probe, undertaking the assay, and analyzing the data obtained from flow cytometry.