Advanced therapy medicinal products (ATMPs) represent a new generation of biopharmaceuticals that comprise gene therapy medicinal products (GTMPs), somatic cell therapy products (CTMPs), tissue engineered products (TEPs), and combined advanced therapy medicinal products (cATMPs). The joint effort of the academia-industry-regulatory triangle translated scientific progress into ten authorized ATMPs in the European Community. This notion holds promise for the whole field of ATMP therapies that have been increasingly evaluated in a number of clinical studies, also in the Czech Republic (CR). Here, we prepared an overview of regulatory framework, past and present clinical studies, and already authorized ATMPs in the CR. Clinical studies on ATMPs in the CR were mapped using public databases, particularly ClinicalTrials.gov, the European Union Clinical Trials Register, and the State Institute for Drug Control database. We found 50 registered clinical studies using ATMPs in the CR that mostly involve CTMPs (n = 36), followed by GTMPs (n = 4) and TEPs (n = 4). The majority of the studies use autologous ATMPs (76%) and are aimed at the treatment of oncologic conditions (58%) and musculoskeletal disorders (24%). The most frequent autologous cell type was dendritic cells (42%), bone marrow mononuclear cells (16%) and bone marrow mesenchymal stromal cells (13%). Allogeneic ATMPs (12%) are mostly aimed at the treatment of venous ulcers (33%) and utilize keratinocytes and fibroblasts (33%). In summary, ATMPs are increasingly tested in clinical trials in the CR, which will most likely lead to their translation into broader clinical use. However, to stimulate market viability of registered ATMPs, implementation of the sophisticated reimbursement system will be required.