Unmanned Aerial Vehicles (UAVs) are increasingly being integrated into a wide range of industries and ap- plications, including but not limited to surveillance, logistics, environmental monitoring, infrastructure inspection, and disaster management. The growing deployment of UAVs in both civilian and defence sectors highlights their versatil- ity and operational efficiency. However, one of the core enablers of UAV functionality is their dependence on wireless communication systems and network protocols to facilitate control, telemetry, and coordination with ground control sta- tions or other UAVs. This reliance on open and often unsecured communication channels exposes UAVs to a variety of significant security threats. This paper focuses on performing a comprehensive vulnerability analysis of the MAVLink protocol, which is currently the most extensively adopted communication protocol for UAVs. We analyse key security weaknesses inherent in the MAVLink protocol’s design, as well as additional vulnerabilities that may arise from specific implementations of the protocol. These vulnerabilities can enable a wide range of potential attacks, including spoofing, message injection, replay attacks, and unauthorised access. In addition, we assess the effectiveness of existing security mechanisms that have been proposed or implemented, such as encryption techniques, authentication frameworks, and intrusion detection systems. By systematically highlighting these vulnerabilities and their real-world implications, this study aims to offer meaningful insights into improving MAVLink protocol security and fostering more resilient and secure UAV communication systems.