The data assimilation module of the Regional Atmospheric Modeling System (RAMS) was operationally used during the September-October 2002 RACCI campaign in Rondonia, located in the southern portion of the Amazon Basin in the transition from the forest to pasture. The analysis was performed with a course grid with 80 km resolution and a fine grid of 20 km over the area of interest. Nudging towards the NCEP analysis was applied at the borders of the coarse grid and very week nudging was maintained during the assimilation cycle. The scheme was stable and provided realistic estimates of the low level flow during the campaign. A comparison with observed surface and upper air data indicates that the downscaling significantly reduces the analysis bias. A separate comparison is provided by the bias between the model precipitation and the satellite derived data (TRMM) and the comparison with the surface fluxes provided by the micrometeorological towers. The diurnal variation of the low level flow as well as of the precipitation were also reasonably reproduced by the mesoscale reanalysis.