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This paper describes an optimal length and combination of short shield ducts to prevent the leakage of magnetic flux through the openings of a double-layered magnetically shielded room (MSR) used for electron-beam lithography systems and biomagnetic measurements. A number of openings as large as 500 times 500 mm must be provided in the walls, ceiling, and floor of such MSRs for air conditioning and cables. First, the magnetic field leakage from the openings, using a small model of an MSR, was measured with short shield ducts of various lengths in order to confirm the validity of the analysis and practical realization. Next, the distributions of the magnetic fields inside the small model were evaluated using 3-D magnetic field analysis and the finite element method. The method of analysis was verified by comparing computed results with those measured. We show the optimal length of shield duct attached around the openings as follows: The optimal combination of short shield ducts is an outer layer duct which is the same length as the width of the opening with an inner layer duct which is half the length of the opening. These lengths of duct accord with the optimal lengths when the outer and inner layer ducts are employed as a single duct. The leakage flux of the optimal single duct through the opening can be decreased to a half by the optimal combination of shield ducts. This also corresponds to the fact that the length of the inner layer duct should not protrude from the outer layer in order to avoid collecting surplus fluxes outside the magnetically shielded room.