Abstract This article presents a computerized multi-criteria evaluation system for assembly sequences, which evaluates all feasible assembly sequences based on ease of assembly criteria and finds the most efficient assembly sequence in the Flexible Assembly Systems (FAS) environment. The proposed system, called CASES (Computer-aided Assembly Sequence Evaluation System), automatically evaluates assembly sequences in two stages: (1) Evaluation based on assembly activity performance and (2) Evaluation based on the FAS performance. The first stage of CASES aims to reduce the solution space of all the feasible assembly sequences and finds only promising feasible sequences. The evaluation criteria are based on assembly activity performance such as equipment constraints, ease of part handling, ease of part joining, and the number of tool changes during an assembly process. With the reduced set of assembly sequences, the second stage finds the most efficient assembly sequence in the FAS environment. For evaluation based on the FAS performance, CASES solves a scheduling problem, MFASSP (Modified FAS Scheduling Problem), to find an assembly sequence which provides the minimal makespan. CASES is illustrated with a real assembly.