Different sources of uncertainty in CFD simulations are illustrated by a detailed study of two-dimensional, turbulent, transonic flow in converging-diverging channel. Runs were performed with the commercial CFD code GASP using different turbulence models, grid levels, and flux-limiters to see the effect of each on the CFD simulation uncertainties. Two flow conditions were studied by changing the exit pressure ratio: the first is a complex case with a strong shock and a separated flow region, the second is the weak shock case with no separation. The uncertainty in CFD simulations has been studied in terms of four contributions: (1) discretization error, (2) error in geometry representation, (3) turbulence model, and (4) the downstream boundary condition. In this paper, we have quantified the relative contribution and the importance of each source of uncertainty and shown the level of scatter in results that a well informed CFD user may obtain in a typical design activity. The nozzle efficiency results obtained in this study showed that the range of variation for the strong shock case was much larger than that observed in the weak shock case. The discretization errors were up to 6% and the relative uncertainty originating from the selection of different turbulence models was as large as 9% for the strong shock case. Furthermore, the results demonstrated that grid convergence is not achieved with grid levels that have moderate mesh sizes and showed that highly refined grids are required to obtain solutions with an acceptable level of accuracy in design problems that involve simulations of complex flow fields. The results illustrated the interaction of different sources of uncertainty and showed that the magnitudes of numerical errors are influenced by the physical models used.