There are substantial uncertainties in processes influencing aerosol and precursor distributions, however, that have not yet been resolved through comparisons with observations. In this study, we examine the impact of the uncertainty in injection heights of emissions in the Community Atmosphere Model version 5 (CAM5), an aerosol-climate model, equipped with an explicit aerosol source tagging technique. We quantity the spatial and temporal ranges of modeled near-surface concentrations of SO₂ (precursor of sulfate) and aerosols (sulfate, black carbon and primary organic matter) due to the uncertainty in injection height of emissions from industrial and international shipping sectors. CAM5 simulations indicate that the assumed effective anthropogenic emission height is very important to SO₂ near-surface concentrations and vertical profile. The global range of near-surface SO₂concentration over land (ocean) due to uncertainty in industrial (international shipping) emission injection height is 81% (76%), relative to the average concentration. This sensitivity is much larger than the uncertainty of SO₂ emission rates. Black carbon and primary organic matter concentration and profiles are also sensitive to emission heights (53% over land and 28% over oceans). The impact of emission height uncertainty is larger in winter for land-based emissions, but larger in summer over the northern hemisphere ocean for shipping emissions. The variation in aerosol optical depth related to shipping emission injection heights is 11% over oceans, revealing the potential importance of injection height on aerosol forcing and climatic effects. The large impact on SO₂ concentrations can confound attempts to use surface, aircraft, and satellite observations to constrain the importance of other processes that govern sulfur compound distributions in the atmosphere. The influence of emission height on vertical SO₂column also will impact the accuracy of satellite retrievals.