A significant seasonality in stratomesospheric CO (24–100 km) above mid-latitudes is derived from FTIR via a new regularization scheme. Half hourly means from the Zugspitze (47.42°N, 10.98°E, 2964 m a.s.l.) and nearby Garmisch (745 m a.s.l.) measurements show excellent agreement (R = 0.94, slope 0.91, standard deviation 12%). Mean seasonality of the Zugspitze series (1999–2008) shows a November–April enhancement (February maximum 3.63 × 10¹⁶ cm⁻²) and a summer background (1.64 × 10¹⁶ cm⁻²) which agrees with the WACCM model. Measured monthly means reveal a year-to-year variability of up to 32% (1-sigma) in winter not reproduced by WACCM (R = −0.13). Frequency distributions of daily means are right skewed in winter due to enhancements by vortex air transport (1–3 days duration) which typically reflect CO levels of the vortex border and may even reach vortex-center levels (≈300% of the multi-annual monthly median).