Adhesively bonded repairs provide a highly structurally efficient and cost-effective means of restoring residual strength to aircraft components. However, gaining airworthiness approval for bonded repairs to primary structures is a significant problem. This is largely because of the failure of current non-destructive inspection techniques to detect weak or non-durable adhesively bonded joints. Due to the presence of undetectable defects and anomalies, recent airworthiness policy ignores the contribution of adhesively bonded joints to the fatigue durability of repaired load-carrying aircraft structures. The key requirement for airworthiness is to demonstrate an acceptable low probability of repair patch disbonding during the remaining life of the structure. In order to satisfy this requirement, it is necessary to identify and control all manufacturing defects and anomalies that influence the durability of the bonded joint. In this study, a methodology has been developed to control manufacturing defects including porosity, unbonded area, and adhesive thickness and flatness variation of bond area. To evaluate the effectiveness of the developed methodology, fatigue tests were conducted, and corresponding uncertainty was analysed. It was found that these defects and anomalies have a significant influence on the fatigue life and fatigue life uncertainty of bonded joints, with minimal effect on their static strength.