Multicellular spheroids are a unique object-model for toxicological studies. Cells in a 3D cluster have microenvironment, intercellular communication, which allows spheroids to be used as more realistic model compared to traditional cell cultures. It is known that tumor microregions consist of heterogeneous populations of cancer cells, in which cell growth and response to antitumor drugs depend on their 3D architecture, intercellular contacts and interaction with the microenvironment. In addition, tumor growth and progression are also strongly influenced by mechanical cues Currently, 3D cell culture models are a powerful tool for studying the toxicity of drug compounds and nanomaterials of different composition and morphology. This review presents data on the use of various techniques, in particular atomic force microscopy, to investigate changes in the mechanical properties of cells in spheroids. In particular, the use of atomic force microscopy as a tool to reveal physicochemical parameters of cells during pathophysiological processes or drug exposure is considered. The relevance of this review is related to the increasing interest in the role of biomechanical properties of tissues, cells and subcellular structures as markers of pathophysiological conditions.