To test the applicability of the scintillation method over a heterogeneous area an experiment was carried out in the summer of 1998 in Flevoland (The Netherlands). In the patchy area only four crops were grown namely sugar beet, potatoes, wheat and onions. From eddy covariance measurements it was found that the heterogeneity was mainly caused by differences in thermal properties. No variations in the aerodynamics roughness length were observed. Two large aperture scintillometers were installed at a height of 11.6 and 20.4 m. A good resemblance was found between the sensible heat fluxes derived from both LAS instruments and the area-averaged fluxes obtained from the in-situ eddy covariance measurements. The slight underestimation of the lower LAS could be assessed using a blending height model and an analytical footprint model. The results also indicated that when scintillometer measurements are made below the blending height the violation to Monin–Obukhov Similarity Theory is small and that reasonable fluxes can be obtained from path-averaged structure parameters.