This work evaluates several techniques to account for mesoscale initial-condition (IC) and model uncertainty in a short-range ensemble prediction system based on the Weather Research and Forecast (WRF) model. A scientific description and verification of several candidate methods for implementation in the U.S. Air Force Weather Agency mesoscale ensemble is presented. Model perturbation methods tested include multiple parametrization suites, land-surface property perturbations, perturbations to parameters within physics schemes and stochastic ‘backscatter’ stream-function perturbations. IC perturbations considered include perturbed observations in 10 independent WRF-3DVar cycles and the ensemble-transform Kalman filter (ETKF). A hybrid of ETKF (for IC perturbations) and WRF-3DVar (to update the ensemble mean) is also tested. Results show that all of the model and IC perturbation methods examined are more skilful than direct dynamical downscaling of the global ensemble. IC perturbations are most helpful during the first 12 h of the forecasts. Physical parametrization diversity appears critical for boundary-layer forecasts. In an effort to reduce system complexity by reducing the number of suites of physical parametrizations, a smaller set of parametrization suites was combined with perturbed parameters and stochastic backscatter, resulting in the most skilful and statistically consistent ensemble predictions.