During the NOAA Southern Oxidant Study 1999 (SOS1999), Texas Air Quality Study 2000 (TexAQS2000), International Consortium for Atmospheric Research on Transport and Transformation (ICARTT2004), and Texas Air Quality Study 2006 (TexAQS2006) campaigns, airborne measurements of isoprene and monoterpenes were made in the eastern United States and in Texas, and the results are used to evaluate the biogenic emission inventories BEIS3.12, BEIS3.13, MEGAN2, and WM2001. Two methods are used for the evaluation. First, the emissions are directly estimated from the ambient isoprene and monoterpene measurements assuming a well-mixed boundary layer and are compared with the emissions from the inventories extracted along the flight tracks. Second, BEIS3.12 is incorporated into the detailed transport model FLEXPART, which allows the isoprene and monoterpene mixing ratios to be calculated and compared to the measurements. The overall agreement for all inventories is within a factor of 2 and the two methods give consistent results. MEGAN2 is in most cases higher, and BEIS3.12 and BEIS3.13 lower than the emissions determined from the measurements. Regions with clear discrepancies are identified. For example, an isoprene hot spot to the northwest of Houston, Texas, was expected from BEIS3 but not observed in the measurements. Interannual differences in emissions of about a factor of 2 were observed in Texas between 2000 and 2006.