This paper considers the optimal element sequencing in a linear multi‐state multiple sliding window system that consists of n linearly ordered multi‐state elements. Each multi‐state element can have different states: from complete failure up to perfect functioning. A performance rate is associated with each state. The failure of type i in the system occurs if for any i (1=i=I) the cumulative performance of any r
i
consecutive elements is lower than w
i
. The element sequence strongly affects the probability of any type of system failure. The sequence that minimizes the probability of certain type of failure can provide high probability of other types of failures. Therefore the optimization problem for the multiple sliding window system is essentially multi‐objective. The paper formulates and solves the multi‐objective optimization problem for the multiple sliding window systems. A multi‐objective Genetic Algorithm is used as the optimization engine. Illustrative examples are presented.