The generalized likelihood ratio test (GLRT) is a statistical fault detection method used for revealing fault occurrences in electronic systems. In this paper, the GLRT technique is analysed and customized for a rubidium frequency standard in order to reveal mean or standard deviation changes in the clock frequency. Experimental results are presented that confirm the effectiveness of the technique also when it is applied to data acquired from a rubidium clock. Monte Carlo simulations are shown in order to characterize the proposed method and to give a simple interpretation of the obtained results. The effectiveness of the GLRT has been already compared with standard tools such as the Allan variance (Nunzi E et al 2007 IEEE Trans. Instrum. Meas. 56 523–8). In particular, the sensitivity of the method with respect to the jump size has been analysed. In this paper, the fault detection technique is characterized with respect to its readiness in terms of the number of samples employed for obtaining a failure occurrence when applied to clock frequency. Results obtained are employed for giving practical indications on the design of this failure test.