A three-dimensional finite element model of a three-bolt, single-lap composite joint is constructed using the non-linear finite element code MSC.Marc. The model is validated against an experiment where the load distribution in the joint is measured using instrumented bolts. Two different joint configurations are examined, one with neat-fit clearances at each bolt-hole and another with a 240 µm clearance at one hole with neat-fits at the others. Bearing and by-pass stresses are extracted from the model and used in conjunction with published bearing/by-pass diagrams to predict the failure load, mode and location for the joints. It is shown that the proposed model accurately predicts the failure behaviour of the joints, as determined from experiments on three-bolt joints loaded to failure. It is also shown that introducing a clearance into one hole significantly changes the failure sequence, but does not affect the ultimate failure load, mode or location. The proposed method demonstrates a simple approach to predicting damage in complex multi-bolt composite joints.