Lanthanide-based upconversion nanoparticles (UCNPs) have been widely explored in various fields, including optical imaging, in recent years. Although earlier work has shown that UCNPs with different lanthanide (Ln3+) dopants exhibit various colors, multicolor-especially in vivo multiplexed biomedical imaging-using UCNPs has rarely been reported. In this work, we synthesize a series of UCNPs with different emission colors and functionalize them with an amphiphilic polymer to confer water solubility. Multicolor in vivo upconversion luminescence (UCL) imaging is demonstrated by imaging subcutaneously injected UCNPs and applied in multiplexed in vivo lymph node mapping. We also use UCNPs for multicolor cancer cell labeling and realize in vivo cell tracking by UCL imaging. Moreover, for the first time we compare the in vivo imaging sensitivity of quantum dot (QD)-based fluorescence imaging and UCNP-based UCL imaging side by side, and find the in vivo detection limit of UCNPs to be at least one order of magnitude lower than that of QDs in our current non-optimized imaging system. Our data suggest that, by virtue of their unique optical properties, UCNPs have great potential for use in highly-sensitive multiplexed biomedical imaging.