Abstract Cloud detection in optical remote sensing images is a crucial problem because undetected clouds can produce misleading results in the analyses of surface and atmospheric parameters. Sentinel-2 provides high spatial resolution satellite data distributed with associated cloud masks. In this paper, we evaluate the ability of Sentinel-2 Level-1C cloud mask products to discriminate clouds over a variety of biogeographic scenarios and in different cloudiness conditions. Reference cloud masks for the identification of misdetection were generated by applying a local thresholding method that analyses Sentinel-2 Band 2 (0.490 μm) and Band 10 (1.375 μm) separately; histogram-based thresholds were locally tuned by checking the single bands and the natural color composite (B4B3B2); in doubtful cases, NDVI and DEM were also analyzed to refine the masks; the B2B11B12 composite was used to separate snow. The analysis of the cloud classification errors obtained for our test sites allowed us to get important inferences of general value. The L1C cloud mask generally underestimated the presence of clouds (average Omission Error, OE, 37.4%); this error increased (OE > 50%) for imagery containing opaque clouds with a large transitional zone (between the cloud core and clear areas) and cirrus clouds, fragmentation emerged as a major source of omission errors (R2 0.73). Overestimation was prevalently found in the presence of holes inside the main cloud bodies. Two extreme environments were particularly critical for the L1C cloud mask product. Detection over Amazonian rainforests was highly inefficient (OE > 70%) due to the presence of complex cloudiness and high water vapor content. On the other hand, Alpine orography under dry atmosphere created false cirrus clouds. Altogether, cirrus detection was the most inefficient. According to our results, Sentinel-2 L1C users should take some simple precautions while waiting for ESA improved cloud detection products
