Three-dimensional (3D) culture systems, which include spheroids (SPs), provide a unique platform for studying complex biological processes in vivo and for enhancing the capabilities of in vitro test systems. Their uniqueness lies in the 3D organization of cells and in the reproduction of complex intercellular interactions, similar to those in native tissues and organs. These mini-organs can be used for fundamental research, tissue-engineering constructs, development of preclinical models for testing pharmacological drugs, etc. Important and current issues regarding SPs involve improving methods for their production and cryopreservation. Solving these issues will expand the range and effectiveness of their use in tissue engineering. Here, we describe the authors' research and experience on factors influencing the formation of SPs, which can enhance the understanding of their correct application and standardization. A crucial aspect of this review is the information on applying theoretical approaches based on physico-mathematical calculations to improve the quality of existing cryopreservation protocols for SPs. https://doi.org/10.54680/fr25110110112.