The combination of low anthropogenic emissions and large biogenic sources that characterizes the Southern Hemisphere (SH) leads to significant differences in atmospheric composition relative to the better studied Northern Hemisphere. This unique balance of sources poses significant challenges for global models. Carbon monoxide (CO) in particular is difficult to simulate in the SH due to the increased importance of secondary chemical production associated with the much more limited primary emissions. Here, we use aircraft observations from the 1991–2000 Cape Grim Overflight Program (CGOP) and the 2009–2011 HIAPER (High-performance Instrumented Airborne Platform for Environmental Research) Pole-to-Pole Observations (HIPPO), together with model output from the SH Model Intercomparison Project, to elucidate the drivers of CO vertical structure in the remote SH. Observed CO vertical profiles from Cape Grim are remarkably consistent with those observed over the southern mid-latitudes Pacific 10–20 years later, despite major differences in time periods, flight locations, and sampling strategies between the two data sets. These similarities suggest the processes driving observed vertical gradients are coherent across much of the remote SH and have not changed significantly over the past 2 decades. Model ability to simulate CO profiles reflects the interplay between biogenic emission sources, the chemical mechanisms that drive CO production from these sources, and the transport that redistributes this CO throughout the SH. The four chemistry-climate and chemical transport models included in the intercomparison show large variability in their abilities to reproduce the observed CO profiles. In particular, two of the four models significantly underestimate vertical gradients in austral summer and autumn, which we find are driven by long-range transport of CO produced from oxidation of biogenic compounds. Comparisons between the models show that more complex chemical mechanisms do not necessarily provide more accurate simulation of CO vertical gradients due to the convolved impacts of emissions, chemistry, and transport. Our results imply a large sensitivity of the remote SH troposphere to biogenic emissions and chemistry, both of which remain key uncertainties in global modeling. We suggest that the CO vertical gradient can be used as a metric for future model evaluation as it provides a sensitive test of the processes that define the chemical state of the background atmosphere.