Abstract This paper examines discrepancies between cloud optical thickness (COT) retrievals from the Moderate Resolution Imaging Spectroradiometer (MODIS) cloud product, and cloud opacity measurements from the Cloud‐Aerosol Lidar with Orthogonal Polarization (CALIOP) lidar. The statistical analysis of a yearlong data set of collocated MODIS‐CALIOP retrievals reveals a striking discrepancy: many single‐layer liquid‐phase cloud pixels identified as transparent by CALIOP exhibit extremely high COT values (>100) in MODIS retrievals. These cloud retrievals are referred to as anomalous opaque clouds (AOCs). Investigations reveal that AOCs frequently occur over mid‐ and high‐latitude regions of the globe, where the Sun is typically low. The three dimensional (3‐D) radiative effects as a potential cause of these AOCs are discussed.