We present south polar winter infrared observations from the Mars Climate Sounder (MCS) and test three hypotheses concerning the origins of “cold spots”: regions of anomalously low infrared brightness temperatures, which could be due to enrichment in non-condensable gases, low-emissivity surface frost, or optically thick CO2 clouds. Clouds and surface frosts have been historically difficult to distinguish, but the unique limb sounding capability of MCS reveals extensive tropospheric CO2 clouds over the cold spots. We find that both clouds and surface deposits play a significant role in lowering the infrared emissivity of the seasonal ice cap, and the granular surface deposits are likely emplaced by snowfall. Surface temperatures indicate the polar winter atmosphere is enriched by a factor ∼5–7 in non-condensable gases relative to the annual average, consistent with earlier gamma ray spectrometer observations, but not enough to account for the low brightness temperatures. A large ∼500-km diameter cloud with visible optical depth ∼0.1–1.0 persists throughout winter over the south polar residual cap (SPRC). At latitudes 70–80°S, clouds and low emission regions are smaller and shorter-lived, probably corresponding to large-grained “channel 1” clouds observed by the Mars Orbiter Laser Altimeter. Snowfall over the SPRC imparts the lowest emissivity in the south polar region, which paradoxically tends to reduce net accumulation of seasonal CO2 by backscattering infrared radiation. This could be compensated by the observed anomalously high summertime albedo of the SPRC, which may be related to small grains preserved in a rapidly formed snow deposit.