Three-dimensional cloud-resolving model simulations of a mesoscale region around Kwajalein Island during the Kwajalein Experiment (KWAJEX) are performed. Using observed winds along with surface and large-scale thermodynamic forcings, the model tracks the observed mean thermodynamic soundings without thermodynamic nudging during 52-day simulations spanning the whole experiment time period, 24 July–14 September 1999. Detailed comparisons of the results with cloud and precipitation observations, including radar reflectivities from the Kwajalein ground validation radar and International Satellite Cloud Climatology Project (ISCCP) cloud amounts and radiative fluxes, reveal the biases and sensitivities of the model’s simulated clouds. The amount and optical depth of high cloud are underpredicted by the model during less rainy periods, leading to excessive outgoing longwave radiation (OLR) and insufficient albedo. The simulated radar reflectivities tend to be excessive, especially in the upper troposphere, suggesting that simulated high clouds are precipitating large hydrometeors too efficiently. Occasionally, large-scale advective forcing errors also seem to contribute to upper-level cloud and relative humidity biases. An extensive suite of sensitivity studies to different microphysical and radiative parameterizations is performed, with surprisingly little impact on the results in most cases.