Diagnosis of actuator faults is crucial for aircraft since loss of actuation can have catastrophic consequences. For autonomous aircraft the steps necessary to achieve fault tolerance is limited when only basic and non-redundant sensor and actuators suites are present. Through diagnosis that exploits analytical redundancies it is, nevertheless, possible to cheaply enhance the level of safety. This paper presents a method for diagnosing control surface faults by using basic sensors and hardware available on an autonomous aircraft. The capability of fault diagnosis is demonstrated obtaining desired levels of false alarms and detection probabilities. Self-tuning residual generators are employed for diagnosis and are combined with statistical change detection to form a setup for robust fault diagnosis. On-line estimation of test statistics is used to obtain a detection threshold and a desired false alarm probability. A data based method is used to determine the validity of the methods proposed. Verification is achieved using real data and shows that the presented diagnosis method is efficient and could have avoided incidents where faults led to loss of aircraft. ; (c) 2013 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other users, including reprinting/ republishing this material for advertising or promotional purposes, creating new collective works for resale or redistribution to servers or lists, or reuse of any copyrighted components of this work in other works.