According to the results of review of the regulatory legal acts and standardization documents, the necessity has been determined to develop a methodology for risk assessment in production of functional food products and its introduction into operation for implementation of the quality control system of food products fortified with iodine. This article represents the description of development of risk assessment methodology assigned for assessing the quality control system for functional foods fortified with iodine. The hazardous event in this case is the non-compliance of the food product with the regulatory requirements, in particular the decrease of iodine content in the functional foods down to a level below 30 mcg/100g of the product, which is less than 15% of an adult person's daily requirement. To assess the probable risks that can affect the peculiar features of the functional foods, RCA root cause mapping system was proposed that includes the standard methods: Ishikawa cause and effect diagram, fault tree analysis FTA, failure mode and effect analysis FMEA, and Pareto analysis. The technology of producing of the cooked sausages fortified with iodine-containing food ingredients was chosen as the object of research, as this technology is associated with a wide variety of technological modes and methods of raw materials processing, as well as the storage conditions of the ready products. The results of the study included a review of the collected data, consideration of the hypothesis, expert opinion on the most probable root causes of failures and losses, and the recommended preventive and corrective actions.