Photothermal ablation based on resonant illumination of near-infrared-absorbing noble metal nanoparticles that have accumulated in tumors is a highly promising cancer therapy, currently in multiple clinical trials. A crucial aspect of this therapy is the nanoparticle size for optimal tumor uptake. A class of nanoparticles known as hollow Au (or Au–Ag) nanoshells (HGNS) is appealing because near-IR resonances are achievable in this system with diameters less than 100 nm. However, in this study, we report a surprising finding that in vivo HGNS are unstable, fragmenting with the Au and the remnants of the sacrificial Ag core accumulating differently in various organs. We synthesized 43, 62, and 82 nm diameter HGNS through a galvanic replacement reaction, with nanoparticles of all sizes showing virtually identical NIR resonances at ∼800 nm. A theoretical model indicated that alloying, residual Ag in the nanoparticle core, nanoparticle porosity, and surface defects all contribute to the presence of the plasmon resonance at the observed wavelength, with the major contributing factor being the residual Ag. While PEG functionalization resulted in stable nanoparticles under laser irradiation in solution, an anomalous, strongly element-specific biodistribution observed in tumor-bearing mice suggests that an avid fragmentation of all three sizes of nanoparticles occurred in vivo. Stability studies across a wide range of pH environments and in serum confirmed HGNS fragmentation. These results show that NIR resonant HGNS contain residual Ag, which does not stay contained within the HGNS in vivo. This demonstrates the importance of tracking both materials of a galvanic replacement nanoparticle in biodistribution studies and of performing thorough nanoparticle stability studies prior to any intended in vivo trial application.