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Computational fluid dynamics (CFD) is frequently used to support the design of naturally ventilated buildings; however, the model accuracy should be thoroughly assessed, ideally through validation with full-scale measurements. The present study aims to (1) validate transient CFD simulations with uncertainty quantification (UQ) for buoyancy-driven natural ventilation against full-scale experiments in an operational atrium building, and (2) quantify the sensitivity of the CFD results to the thermal boundary conditions. The UQ and sensitivity analysis consider uncertainties in the initial and boundary conditions for the temperatures. Considering the volume-averaged air temperature on each floor, the predictions and measurements agree well with discrepancies less than 0.3 °C. When considering the temperature averaged over smaller zones on each floor, two trends can be observed. First, in zones not adjacent to windows, the discrepancies between the CFD and measurements can be explained by uncertainty in the boundary conditions and the measurements. Second, in zones adjacent to windows, higher discrepancies are observed due to oscillations in the inflow jets just downstream of the windows, and due to geometrical simplifications in the CFD model. The sensitivity analysis demonstrates that the boundary conditions for the thermal mass surface temperature and the outdoor temperature have a dominant effect on the indoor air temperature predictions, with their relative importance varying as function of proximity to the windows.