Large-scale mapping of the Brazilian Savanna (Cerrado) vegetation using remote sensing images is still a challenge due to the high spatial variability and spectral similarity of the different characteristic vegetation types (physiognomies). In this paper, we report on semantic segmentation of the three major groups of physiognomies in the Cerrado biome (Grasslands, Savannas and Forests) using a fully convolutional neural network approach. The study area, which covers a Brazilian conservation unit, was divided into three regions to enable testing the approach in regions that were not used in the training phase. A WorldView-2 image was used in cross validation experiments, in which the average overall accuracy achieved with the pixel-wise classifications was 87.0%. The F-1 score values obtained with the approach for the classes Grassland, Savanna and Forest were of 0.81, 0.90 and 0.88, respectively. Visual assessment of the semantic segmentation outcomes was also performed and confirmed the quality of the results. It was observed that the confusion among classes occurs mainly in transition areas, where there are adjacent physiognomies if a scale of increasing density is considered, which agrees with previous studies on natural vegetation mapping for the Cerrado biome. © Authors 2020. All rights reserved.