Peroxy radicals were measured onboard two scientific aircrafts during the AMMA (African Monsoon Multidisciplinary Analysis) campaign in summer 2006. This paper reports results from the flight on 16 August 2006 during which measurements of HO by laser induced fluorescence spectroscopy at low pressure (LIF-FAGE) and total peroxy radicals (RO* =HO +sRO , R = organic chain) by two similar instruments based on the peroxy radical chemical amplification (PeRCA) technique were subject of a blind intercomparison. The German DLR-Falcon and the British FAAM-BAe-146 flew wing tip to wing tip for about 30 min making concurrent measurements on 2 horizontal level runs at 697 and 485 hPa over the same geographical area in Burkina Faso. A full set of supporting measurements comprising photolysis frequencies, and relevant trace gases like CO, NO, NO , NO , O and a wider range of VOCs were collected simultaneously. Results are discussed on the basis of the characteristics and limitations of the different instruments used. Generally, no data bias are identified and the RO* data available agree quite reasonably within the instrumental errors. The [RO* ]/ [HO ] ratios, which vary between 1:1 and 3:1, as well as the peroxy radical variability, concur with variations in photolysis rates and in other potential radical precursors. Model results provide additional information about dominant radical formation and loss processes. © 2010 Author(s).