A diverse array of carbon nanomaterials (NMs), including fullerene, carbon nanotubes (CNTs), graphene, nanodiamonds, and carbon nanoparticles, have been discovered and widely applied in a variety of industries. Carbon NMs have been detected in the environment and have a strong possibility of entering the human body. The safety of carbon NMs has thus become a serious concern in academia and society. To achieve strict biosafety assessments, researchers need to fully understand the effects and fates of NMs in the human body, including information about absorption, distribution, metabolism, excretion, and toxicity (ADME/T). To acquire the ADME data, researchers must quantify NMs, but carbon NMs are very difficult to quantify in vivo. The carbon background in a typical biological system is high, particularly compared with the much lower concentration of carbon NMs. Moreover, carbon NMs lack a specific detection signal. Therefore, isotopic labeling, with its high sensitivity and specificity, is the first choice to quantify carbon NMs in vivo. Previously, researchers have used many isotopes, including ¹³C, ¹⁴C, ¹²⁵I, ¹³¹I, ³H, ⁶⁴Cu, ¹¹¹In, ⁸⁶Y, 99mTc, and ⁶⁷Ga, to label carbon NMs. We used these isotopic labeling methods to study the ADME of carbon NMs via different exposure pathways in animal models. Except for the metabolism of carbon NMs, which has seldom been investigated, significant amounts of data have been reported on the in vivo absorption, distribution, excretion, and toxicity of carbon NMs, which have revealed characteristic behaviors of carbon NMs, such as reticuloendothelial system (RES) capture. However, the complexity of the biological systems and diverse preparation and functionalization of the same carbon NMs have led to inconsistent results across different studies. Therefore, the data obtained so far have not provided a compatible and systematic profile of biosafety. Further efforts are needed to address these problems. In this Account, we review the in vivo quantification methods of carbon NMs, focusing on isotopic labeling and tracing methods, and summarize the related labeling, purification, bio-sampling, and detection of carbon NMs. We also address the advantages, applicable situations, and limits of various labeling and tracing methods and propose guidelines for choosing suitable labeling methods. A collective analysis of the ADME information on various carbon NMs in vivo would provide general principles for understanding the fate of carbon NMs and the effects of chemical functionalization and aggregation of carbon NMs on their ADME/T in vivo and their implications in nanotoxicology and biosafety evaluations.