Food safety assurance is one of the most important and significant issues in the activity of the food sector. Product certification process according to various standards means the highest quality not only for the company but for the consumer as well. Company's executives are free to choose what a management system should be introduced in the organization. It must be effective and viable. International standards and modern quality management systems have been developed and currently are widely used to accomplish this task. In order to ensure the highest quality requirements in all food supply chain, companies often implement and integrate quality, environmental and food safety management. However, the company's executives faces many difficulties to select which of the management systems is superior and the most appropriate for certain company. This paper analyses the requirements of the international standards towards the food safety and quality for the establishment of food quality and food safety management systems; similarities and differences between them, to evaluate the application of these systems, the main advantages and disadvantages. Implementation of the quality and safety management systems in Lithuanian food companies was analysed. At least one management system is certified at the 87 Lithuanian food companies. Of these, the management system according to the ISO 9001:2015 standard is certified at 48 companies, according to the ISO 22000:2005 -at 53 companies, and according to the requirements of the British Retail Consortium standard -at 31 companies. Even 45% of the companies have implemented and are certified by two or more mutually integrated management systems.