Abstract: In Wireless Sensor Networks (WSNs), it is of great importance for fault diagnosis in the WSNs to ensure the accuracy of the information collected from the network, for the low cost and the deployment of a large number of sensor nodes in uncontrolled or harsh or hostile environments. In this study, we have presented a protocol, named CRFDA (Cluster-Based Real-time Fault Diagnosis aggregation algorithm for WSNs), which is based on the comparison approach aiming at achieving a correct and complete diagnosis for hierarchical WSNs. CRFDA is based on clustering in the network which can be carried out simultaneously in all cluster. Besides, it is a real-time diagnosis method and can be spontaneously implemented in each round. It is known from CRFDA that both hard and soft faults can be diagnosed correctly in the finite time. Algorithm correctness, communication complexity and time complexity proofs are presented in this study. Compared with other existing protocols, CRFDA performs better. We have also developed a simulator by NS-2 (using LEACH) to analyze the correctness of our algorithm. The simulation results show that our algorithm is a correct and efficient fault diagnosis algorithm in WSNs.