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Phenotypes observed in a large cohort of patients with cone and cone-rod dystrophies (COD/CORDs) are described based on multimodal retinal imaging features in order to help in analyzing massive next-generation sequencing data. Structural abnormalities of 58 subjects with molecular diagnosis of COD/CORDs were analyzed through specific retinal imaging including spectral-domain optical coherence tomography (SD-OCT) and fundus autofluorescence (BAF/IRAF). Findings were analyzed with the underlying genetic defects. A ring of increased autofluorescence was mainly observed in patients with <i>CRX</i> and <i>GUCY2D</i> mutations (33% and 22% of cases respectively). &#8220;Speckled&#8221; autofluorescence was observed with mutations in three different genes (<i>ABCA4</i> 64%; <i>C2Orf71</i> and <i>PRPH2</i>, 18% each). Peripapillary sparing was only found in association with mutations in <i>ABCA4</i>, although only present in 40% of such genotypes. Regarding SD-OCT, specific outer retinal abnormalities were more commonly observed in particular genotypes: focal retrofoveal interruption and <i>GUCY2D</i> mutations (50%), foveal sparing and <i>CRX</i> mutations (50%), and outer retinal atrophy associated with hyperreflective dots and <i>ABCA4</i> mutations (69%). This study outlines the phenotypic heterogeneity of COD/CORDs hampering statistical correlations. A larger study correlating retinal imaging with genetic results is necessary to identify specific clinical features that may help in selecting pathogenic variants generated by high-throughput sequencing.