A successful observing system simulation experiment (OSSE) is fundamentally dependent on the simulation of the global observing system used in the experiment. In many applications, a free-running numerical model simulation, called a nature run, is used as the meteorological truth from which the observations are simulated. To accurately and realistically simulate observations from any nature run, the simulated observations must contain realistic cloud effects representative of the meteorological regimes being sampled. This study provides a validation of the clouds in the Joint OSSE nature run generated at ECMWF. Presented is the methodology used to validate the nature run cloud fraction fields with seasonally aggregated combined CloudSat/Cloud–Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) cloud geometric profile retrievals and the Wisconsin High Resolution Infrared Radiation Sounder (HIRS) cloud climatology. The results show that the Joint OSSE nature run has a correct vertical distribution of clouds but lacks globally in cloud amount compared to the validation data. The differences between the nature run and validation datasets shown in this study should be considered and accounted for in the generation of the global observing system for use in full OSSE studies.