Measurements of total peroxy radicals (HO2 + RO2) and nitrate radical (NO3) were made on the NOAA research vessel R/V along the U.S. Gulf Coast during the TexAQS 2006 field campaign. The measurements were modelled using a constrained box-model based upon the Master Chemical Mechanism (MCM). The agreement between modelled and measured HO2 + RO2 was typically within similar to 40% and, in the unpolluted regions, within 30%. The analysis of the model results suggests that the MCM might underestimate the concentrations of some acyl peroxy radicals and other small peroxy radicals. The model underestimated the measurements of NO3 by 60-70%, possibly because of rapid heterogeneous uptake of N2O5. The MCM model results were used to estimate the composition of the peroxy radical pool and to quantify the role of DMS, isoprene and alkenes in the formation of RO2 in the different regions. The measurements of HO2 + RO2 and NO3 were also used to calculate the gas-phase budget of NO3 and quantify the importance of organic peroxy radicals as NO3 sinks. RO2 accounted, on average, for 12-28% of the total gas-phase NO3 losses in the unpolluted regions and for 1-2% of the total gas-phase NO3 losses in the polluted regions.