Surface fluxes at a scale of several kilometers are required in many meteorological studies. The scintillation technique is one of the few methods that can provide fluxes at these scales (1 - 10 km). Since usually the earth's surface is heterogeneous at these scales the question arises whether the scintillation method, which is based on the Monin-Obukhov Similarity Theory (MOST), can be applied. To test the applicability of the method over a heterogeneous area an experiment was carried out in Flevoland (The Netherlands). The patchy area consisted of many rectangular plots (500 x 250 m) where four crops were grown namely, sugar beet, potatoes, wheat and onions. Each crop covered 25 % of the area independent of the wind direction (i.e. isotropic conditions). Eddy covariance instruments were placed at four plots, each covered by a different crop, to provide independant surface flux measurements. Based on the eddy covariance measurements it was found that the heterogeneity in the area was caused by variations in thermal properties (i.e. H and LvE). No variation in the surface roughness for momentum was observed. Two Large Aperture Scintillometers (LAS) were placed on two windmills at a height of 11.6 and 20.4 m. The path length of both scintillometers was 2.2 km. A good resemblance was found between the sensible heat fluxes derived from the upper LAS and the area averaged sensible heat fluxes derived from the aggregated in-situ eddy covariance measurements. The slightly lower fluxes from the LAS at 11.6 m could be assessed by using a blending height and a footprint model. After accounting for the spatial distribution of the surface fluxes of the crops in the source area of the LAS the results agreed fairly well. The results have demonstrated that the scintillation method is applicable over heterogenous areas. Also when the scintillometer is measuring below the blending height the violation of the MOST relationship between path averaged structure parameters and fluxes is small and reasonable fluxes can be obtained