Abstract. This paper presents an analytical system for analysis of all single substituted isotopologues ( 12 C 16 O 17 O, 12 C 16 O 18 O, 13 C 16 O 16 O) in nanomolar quantities of CO 2 extracted from stratospheric air samples. CO 2 is separated from bulk air by gas chromatography and CO 2 isotope ratio measurements (ion masses 45 / 44 and 46 / 44) are performed using isotope ratio mass spectrometry (IRMS). The 17 O excess ( 17 O) is derived from isotope measurements on two different CO 2 aliquots: unmodified CO 2 and CO 2 after complete oxygen isotope exchange with cerium oxide (CeO 2 ) at 700 • C. Thus, a single measurement of 17 O requires two injections of 1 mL of air with a CO 2 mole fraction of 390 µmol mol −1 at 293 K and 1 bar pressure (corresponding to 16 nmol CO 2 each). The required sample size (including flushing) is 2.7 mL of air. A single analysis (one pair of injections) takes 15 minutes. The analytical system is fully automated for unattended measurements over several days. The standard deviation of the 17 O excess analysis is 1.7 ‰. Multiple measurements on an air sample reduce the measurement uncertainty, as expected for the statistical standard error. Thus, the uncertainty for a group of 10 measurements is 0.58 ‰ for 17 O in 2.5 h of analysis. 100 repeat analyses of one air sample decrease the standard error to 0.20 ‰. The instrument performance was demonstrated by measuring CO 2 on stratospheric air samples obtained during the EU project RECONCILE with the high-altitude aircraft Geophysica. The precision for RECONCILE data is 0.03 ‰ (1σ ) for δ 13 C, 0.07 ‰ (1σ ) for δ 18 O and 0.55 ‰ (1σ ) for δ 17 O for a sample of 10 measurements. This is sufficient to examine stratospheric enrichments, which at altitude 33 km go up to 12 ‰ for δ 17 O and up to 8 ‰ for δ 18 O with respect to tropospheric CO 2 : δ 17 O ≈ 21 ‰ Vienna Standard Mean Ocean Water (VSMOW), δ 18 O ≈ 41 ‰ VSMOW (Lämmerzahl et al., 2002). The samples measured with our analytical technique agree with available data for stratospheric CO 2 .