Purpose of this paper A new topic that during the last years has come to the attention of researchers is supply chain security. Stakeholders are progressively realizing the importance to join the authority regulations issued by governments (e.g. AEO) to reduce transport delays at Customs or other business certifications (e.g. TAPA) to reduce theft or counterfeiting. However the differences and impacts of security certifications are not always well understood. This paper has the main purpose to explore similarities and diversities of security certifications and to identify their effects on supply chain efficiency and security. Design/methodology/approach This research is based on a system-theoretical approach to describe security certifications, make a comparative analysis and deduct their impact on transport operations. The research design is primarily based on a literature search. Findings The findings put in evidence that authority and business security certifications can be complementary. Moreover transport operators and legislative bodies are recommended to initiate collaboration experiences. Research limitations/implications (if applicable) The comparative analysis will only focus on three main European certifications: the Authorized Economic Operator (AEO), the Freight Security Requirements and the Trucking Security Requirements issued by the Transported Assets Protection Association in Europe (TAPA EMEA). Practical implications (if applicable) The analysis proposed in this paper may support logistics and supply chain managers in the analysis and comparison of authority and business certifications for decision-making. What is original/value of paper Previous research focuses only on the impact of authority security certification programs on transport operations. None of the known literature makes a comparative analysis with existing business certifications to enlighten the different impact on security and efficiency.