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Abstract. Accurate estimation of crop yield before harvest, especially in early growth stages, is important for farmers and researchers to optimize field management and evaluate crop performance. However, existing in-field methods for estimating crop yield are not efficient. The goal of this research was to evaluate the performance of a UAV-based remote sensing system with a low-cost RGB camera to estimate cotton yield based on plant height. The UAV system acquired images at 50 m above ground level over a cotton field at the first flower growth stage. Waypoints and flight speed were selected to allow >70% image overlap in both forward and side directions. Images were processed to develop a geo-referenced orthomosaic image and a digital elevation model (DEM) of the field that was used to extract plant height by calculating the difference in elevation between the crop canopy and bare soil surface. Twelve ground reference points with known height were deployed in the field to validate the UAV-based height measurement. Geo-referenced yield data were aligned to the plant height map based on GPS and image features. Correlation analysis between yield and plant height was conducted row-by-row with and without row registration. Pearson correlation coefficients between yield and plant height with row registration for all individual rows were in the range of 0.66 to 0.96 and were higher than those without row registration (0.54 to 0.95). A linear regression model using plant height was able to estimate yield with root mean square error of 550 kg ha^-1 and mean absolute error of 420 kg ha^-1. Locations with low yield were analyzed to identify the potential reasons, and it was found that water stress and coarse soil texture, as indicated by low soil apparent electricity conductivity (EC_a), might contribute to the low yield. The findings indicate that the UAV-based remote sensing system equipped with a low-cost digital camera was potentially able to monitor plant growth status and estimate cotton yield with acceptable errors.