Abstract. The in situ boundary layer measurement site in Białystok (Poland) has been upgraded with a fully automated observatory for total greenhouse gas column measurements. The automated Fourier Transform Spectrometer (FTS) complements the on-site in situ facilities and FTS solar absorption measurements have been recorded nearly continuously in clear and partially cloudy conditions since March 2009. Here, the FTS measurements are compared with the collocated tall tower data. Additionally, simulations of the Jena CO2 inversion model are evaluated with the Białystok measurement facilities. The simulated seasonal CO2 cycle is slightly overestimated by a mean difference of 1.2 ppm ± 0.9 ppm (1σ) in comparison with the FTS measurements. CO2 concentrations at the surface, measured at the tall tower (5 m, 90 m, 300 m), are slightly underestimated by −1.5 ppm, −1.6 ppm, and −0.7 ppm respectively during the day and by −9.1 ppm, −5.9 ppm, and −1.3 ppm during the night. The comparison of the simulated CO2 profiles with low aircraft profiles shows a slight overestimation of the lower troposphere (by up to 1 ppm) and an underestimation in near-surface heights until 800 m (by up to 2.5 ppm). In an appendix the automated FTS observatory, including the hardware components and the automation software, is described in its basics.