Submicron atmospheric aerosol particles were collected during the Megacity Initiative: Local and Global Research Observation (MILAGRO) in March 2006 at three platforms located in the Mexico City urban area (at the Mexico City Atmospheric Monitoring System building – SIMAT), at about 60 km south-west of the metropolitan area (Altzomoni in the Cortes Pass), and on board the NSF/NCAR aircraft C130. Organic functional group and elemental composition were measured by FTIR and XRF. The average organic mass (OM) concentration, calculated as the sum of organic functional group concentrations, was 9.9 μg m−3 at SIMAT, 6.6 μg m−3 at Altzomoni, and 5.7 μg m−3 on the C130. Aliphatic saturated C-C-H and carboxylic acid COOH groups dominated OM (more than 60%) at the ground sites. On the C130, a non-acid carbonyl C=O, and amine NH2 groups were observed in concentrations above detection limit only outside the Mexico City basin. From the elemental composition of SIMAT samples, we estimated the upper bound of average contribution of biomass burning to the organic carbon (OC) as 33–39%. The average OM/OC ratio was 1.8 at SIMAT, 2.0 at Altzomoni, and 1.6–1.8 on the C130. On the aircraft, higher OM/OC ratios were measured outside of the Mexico City basin, north of the urban area, along the city outflow direction. The average carboxylic acid plus non-acid carbonyl to aliphatic saturated ratio was higher at Altzomoni relative to SIMAT, reflecting a larger average contribution of carbonyl functional groups (largely in carboxylic acids) at the mountain site.