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The fraction of photosynthetically active radiation (FPAR) absorbed by a vegetation canopy is an important variable for global vegetation modelling and is operationally available from data of the Terra Moderate Resolution Imaging Spectroradiometer (MODIS) satellite sensor starting from the year 2000. Product validation is ongoing and important for constant product improvement, but few studies have investigated the specific accuracy of MODIS FPAR using in situ measurements and none have focused on agricultural areas. This study therefore presents a validation of the collection 5 MODIS FPAR product in a heterogeneous agricultural landscape in western Uzbekistan. High-resolution FPAR maps were compiled via linear regression between in situ FPAR measurements and the RapidEye normalized difference vegetation index (NDVI) for the 2009 season. The data were aggregated to the MODIS scale for comparison. Data on the percentage cover of agricultural crops per MODIS pixel allowed investigation of the impact of spatial heterogeneity on MODIS FPAR accuracy. Overall, the collection 5 MODIS FPAR overestimated RapidEye FPAR between approximately 6% and 15%. MODIS quality flags, the underlying biome classification and spatial heterogeneity were investigated as potential sources of error. MODIS data quality was very good in all cases. A comparison of the MODIS land-cover product with high-resolution land-use classification revealed a significant misclassification by MODIS. Yet, we found that the overestimation of MODIS FPAR is independent of classification accuracy. The results indicate that the amount of background information, present even in the most homogeneous pixels (similar to 70% crop cover), is most likely the reason for the overestimation. The behaviour of pure pixels could not be investigated due to a lack of appropriate pixels.