A stochastic finite element-based algorithm for probabilistic analysis of structural systems made of composite sections with random material and geometrical properties under earthquake forces is proposed in this paper. Uncertainties in the structural parameters can be taken into account in this algorithm. For the perturbation-based stochastic finite element method, only the first two moments of random variables need to be known, and is numerically much more efficient and feasible than simulation techniques. The efficiency and accuracy of the proposed algorithm are validated by comparison with results of Monte Carlo simulation method. A summary of stiffness matrix formulation and perturbation-based stochastic finite element dynamic analysis formulation of structural systems made of composite sections is given. These are followed by suitable numerical examples, which indicate that employment of such a dynamic stochastic finite element method leads to significant economical, efficient and accurate solutions for the dynamic analysis of composite structures with stochastic parameters under earthquake forces. Copyright (C) 2010 John Wiley & Sons, Ltd.