OBJECTIVE To describe in detail the structural and functional phenotypes of a patient with cone-rod dystrophy associated with a full deletion of the NPHP1 gene. METHODS A 30-year-old man with a history of end-stage renal disease presented with progressive vision loss in early adulthood prompting evaluation for retinal disease. Ophthalmic evaluation was performed including visual fields, electroretinography, spectral domain optical coherence tomography and short-wavelength and near-infrared fundus autofluorescence imaging. RESULTS The visual acuity was 20/60 in each eye. Fundus examination revealed a subtle bull's-eye maculopathy confirmed with fundus autofluorescence. Spectral domain optical coherence tomography demonstrated perifoveal loss of the outer retinal layers with structural preservation further peripherally. Static perimetry confirmed the loss of cone greater than rod sensitivities in a manner that colocalized to structural findings. Electroretinography revealed decreased cone- and rod-mediated responses. Genetic testing confirmed a homozygous whole-gene deletion of the NPHP1 gene. CONCLUSIONS NPHP1 -associated retinal degeneration may present as a cone-rod dystrophy in addition to the previously reported rod-predominant phenotypes and can notably be associated with systemic abnormalities, including renal disease. Our work further expands on the growing literature describing the retinal disease associated with systemic ciliopathies.