Abstract: SLC46A3 has been identified as a lipid-based nanoparticle-specific biomarker predictive of nanoparticle-cancer cell affinity. SLC46A3 has a strong inverse association with lipid-based nanoparticle uptake across multiple nanoparticle formulations. Tissues with decreased expression levels of SLC46A3 have a greater uptake of lipid-based nanoparticles. The inverse relationship of SLC46A3 expression in tumor tissue and affinity for lipid-based nanoparticles has therapeutic and diagnostic implications, including cancer therapy and diagnosis, and identification of patients most likely to benefit from a lipid-based nanotherapeutic for improved stratification in clinical trials.