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This paper presents a three-dimensional finite-difference time-domain (FDTD) scheme in cylindrical coordinates with an improved algorithm for accommodating the numerical singularity associated with the polar axis. The regularization of this singularity problem is realized based on Faraday's law (for updating the Hr-component) and Ampere's law (for updating the Eφ -, Ez -components). The proposed algorithm has been detailed and verified against a problem with a known solution obtained from a commercial electromagnetic simulation package. The numerical scheme is also illustrated by modeling high-frequency RF field-human body interactions in magnetic resonance imaging (MRI). The results demonstrate the accuracy and capability of the proposed algorithm.