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In this paper we investigate the performance of a downlink multi-carrier code division multiple access (MC-CDMA) system employing a receiver with iterative channel estimation (ICE). The MC-CDMA system transmits M data symbols per user and per orthogonal frequency division multiplexing symbol in parallel, with each data symbol being spread with a Walsh-Hadamard code of length L. Due to the superposition of spread data signals (chips), zero-valued subcarriers can occur, which cannot be used to compute least-squares (LS) channel estimates in ICE. Therefore, we propose the modified LS channel estimation method to overcome this problem and to avoid noise enhancement in ICE. We further investigate the robustness of ICE with the modified LS method if the channel statistics are not known perfectly. Simulation results demonstrate that a signal-to-noise ratio gain of 1 dB can be achieved when employing robust ICE with the modified LS method.