The effect of higher-harmonic fluxes on a subcriticality measurement by the exponential experiment was investigated. An analysis method for obtaining higher-harmonic eigenvalues and eigenfunctions of the neutron diffusion equation of which the eigenvalues are the decay constants in the exponential experiment was developed. We attempted to reproduce three-dimensional neutron flux distributions formed in the exponential experiment with superposition of higher-harmonic fluxes. Exponential experiments were performed for a subcritical rectangular fuel rod array of the TCA (Tank-type Critical Assembly) and the vertical neutron flux distributions at several horizontal locations were measured for various neutron source positions. Higher-harmonic eigenvalues and eigenfunctions in the exponential experiment were calculated to reproduce the vertical neutron fluxes. It was found that they were well reproduced within the fuel rod array or in the water-reflector region close to the array by taking account of the fewer-order harmonic fluxes. The method of higher-harmonic analysis presented in this paper enables us to evaluate the effect of higher-harmonic fluxes or to find measurement conditions such as the arrangement of a neutron source and neutron detectors for obtaining the decay constant of a fundamental mode flux. © 2003 Taylor & Francis Group, Ltd.