Machine Learning (ML) and Artificial Intelligence (AI) methods are used to process and intelligently analyze medical data. The application of ML/AI methods requires specialized sets of labeled medical data of large dimensions. Process organization of quality medical data labeling requires the involvement of a large number assessors and specialists in a particular field of medicine as well as the availability of specialized tools for labeling process optimization considering the specifics of medical data processing. In this paper a universal architectural model of a crowdsourcing system specifically designed for medical data labeling was proposed. The model supports processing of diverse medical data formats, incorporates data anonymization mechanisms and multi-level quality control, while enabling a distributed annotation process with expert community involvement. As a result, classification of actual problems of the process of medical data labeling and data collection, and a quality and safety criteria for comparative analysis of medical data labeling systems was detected and formulated. The scheme of generalized scenario of users’ groups interaction with crowdsourcing system in the context of solving AI problems in the field of medicine was proposed. A universal model of such system architecture was designed and a specialized crowdsourcing system of medical data labeling based on Computer Vision Annotation Tool was implemented on its basis. Testing and approbation of the realized system was carried out at the Pirogov Clinic of High Medical Technologies. The proposed universal model of crowdsourcing system architecture can be used to improve the efficiency and safety of organization and construction of the process of labeling patients’ medical data in the context of solving various applied ML/AI tasks, such as semantic segmentation of internal organs and their pathologies, detection and classification of diseases based on medical images (e.g. computed tomography scans). The developed solution can be used by doctors of various specializations, researchers and developers aimed at the development and creation of methods and technologies of AI in the field of medicine.