A 3-D code for solving the set of Maxwell equations with the finite-difference time-domain method is developed for simulating the propagation and scattering of light in biological cells under realistic conditions. The numerical techniques employed in this code include the Yee algorithm, absorbing boundary conditions, the total field/scattered field formulation, the discrete Fourier transformation, and the near-to-far field transform using the equivalent electric and magnetic currents. The code is capable of simulating light scattering from any real cells with complex internal structure at all angles, including backward scattering. The features of the scattered light patterns in different situations are studied in detail with the objective of optimizing the performance of cell diagnostics employing cytometry. A strategy for determining the optimal angle for measuring side scattered light is suggested. It is shown that cells with slight differences in their intrastructure can be distinguished with two-parameter cytometry by measuring the side scattered light at optimal angles. © 2005 Society of Photo-Optical Instrumentation Engineers.