Interactions between organisms and micro‐ and nano‐sized particles are studied in a relatively new research field—nanopathology. Some diseases (oncological and/or inflammatory) may be connected with accumulation of the particles in the tissues. In general, precise and accurate qualitative evaluation of chemical composition of particles is very important. In such analyses, scanning electron microscopy with energy dispersive X‐ray spectroscopy is used most often. Nevertheless, it reveals merely the elemental composition of particles/clusters. On the other hand, because Raman microspectroscopy is non‐destructive and it is coupled with an optical microscope, it has potential for detection of particles of unknown nature; in addition, it allows determination of the chemical composition of these particles/clusters. Therefore, this technique could be a very useful supporting tool for nanopathology. The aim of the presented study is to survey the possibilities and advantages of Raman microspectroscopy for the detection and characterization of particles of an unknown nature in the samples of human nasal mucosa and amniotic fluids. Three different approaches of analysis are hereby discussed: (1) analysis of the entire area of the sample, (2) division of the sample in sections, and subsequent analysis of a defined number of points in selected parts, and (3) Raman spectral imaging of the selected parts. Results clearly prove high efficiency of Raman microspectroscopy as a tool for characterization of the particles/clusters in human tissues and body fluids, and thus it may allow a better understanding of the potential impact to human health in relation to specific diagnoses. Copyright © 2016 John Wiley & Sons, Ltd.