Nanomaterials have lots of unique physical and chemical properties, such as quantum size effect, surface effect and macroscopic quantum tunnel effect. The biological effects of nanomaterials might be different from those of bulk materials larger than microns even if their chemical compositions are same. Therefore, the biological effects and safety evaluation results obtained from the bulk materials might not be suitable for the nanomaterials. Since 2003, governments worldwide have initiated the researches on biological effects and safety issues of nanomaterials with increasing financial support. China is one of the earliest countries in the world to carry out researches on biological effects and safety issues of nanomaterials. And some research fields have entered the forefront of the world. The CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety established jointly by National Center for Nanoscience and Technology (NCNST) and Institute of High Energy Physics of Chinese Academy of Sciences (IHEP of CAS) was the first professional laboratory focusing on the biological effects and safety of nanomaterials in China. Scientists in this laboratory have done many in-depth studies of the relationship between the physical-chemical properties and biological responses of nanomaterials. They found several factors which affected the biological effects of carbon nanotubes significantly, such as nanoparticle-Crona, metal impurities, surface, size, shape and so on. They have also established multiple models for hazard recognition and risk assessment. Nanomaterials/nanoparticles (NMs/NPs) are exposed to human beings mostly through four routes, i.e., oral intake, skin contact, inhalation, and intravenous injection. Upon entering the body, NMs/NPs are quickly distributed into specific organs and then metabolized primarily by the liver. The final excretion of NMs/NPs usually occurs in the liver and kidney in the form of urine and feces. In general, the most important issues regarding the absorption, distribution, metabolism and excretion (ADME) processes of NMs/NPs include: (1) Where do and how much NMs/NPs get in (via absorption)? (2) Where do and how much NMs/NPs go (via distribution)? (3) How much, when do, and what form of NMs/NPs remain intact (via metabolism)? (4) Where do, how much, and what form of NMs/NPs stay in the system (via excretion)? At various stages of the ADME processes, the challenges for in vivo analysis of NMs/NPs may become largely different. Important analytical methods to resolve the analytical challenges for each absorption, distribution, metabolism and excretion (ADME) process are summarized. The state-of-the art techniques with high sensitivity and high resolution suitable for safety evaluation have been developed to ensure the sustainable development of nanotechnology, such as inductively coupled plasma mass spectrometry (ICPMS), inductively coupled plasma optical emission spectrometry (ICP-OES), nuclear analysis such as neutron activation analysis (NAA), laser ablation inductively coupled plasma mass spectrometry (LAICPMS), secondary ion mass spectrometry (SIMS), synchrotron radiation X-ray fluorescence spectroscopy (SRXRF), X-ray absorption spectroscopy (XAS), X-ray fluorescence spectroscopy (XRF), scanning transmission X-ray microscopy (STXM), transmission X-ray microscopy (TXM) and so on. In this review, we summarize these research progresses in recent years.