Nanotoxicology remains an important and emerging field since only recent years have seen the improvement of biological models and exposure setups toward real-life scenarios. The appropriate analysis of nanomaterial fate in these conditions also required methodological developments in imaging to become sensitive enough and element specific. In the last 2-4 years, impressive breakthroughs have been achieved using electron microscopy, nanoscale secondary ion mass spectrometry, X-ray fluorescence microscopy, or fluorescent sensors. In this review, basics of the approaches and application examples in the study of nanomaterial fate in biological systems will be described to highlight recent successes in the field.