This paper presents a distributed integrated fault diagnosis and accommodation scheme for leader-following formation control of a class of nonlinear uncertain second-order multi-agent systems. The fault model under consideration includes both process and actuator faults, which may evolve abruptly or incipiently. The time-varying leader communicates with a small subset of follower agents, and each follower agent communicates to its directly connected neighbors through a bidirectional network with possibly asymmetric weights. A local fault diagnosis and accommodation component are designed for each agent in the distributed system, which consists of a fault detection and isolation module and a reconfigurable controller module comprised of a baseline controller and two adaptive fault-tolerant controllers, activated after fault detection and after fault isolation, respectively. By using appropriately the designed Lyapunov functions, the closed-loop stability and asymptotic convergence properties of the leader-follower formation are rigorously established under different modes of the fault-tolerant control system. KEYWORDS adaptive control, fault-tolerant control, formation control, multi-agent systems, nonlinear uncertain systems Int J Robust Nonlinear Control. 2018;28:4287-4308.wileyonlinelibrary.com/journal/rnc