To report the association of autoimmune polyglandular syndrome type 1 (APS1) with cone dystrophy in a large Saudi family. This is a Retrospective chart review and prospective genetic testing and ophthalmic examination of a large multiplex consanguineous family. Genetic testing was performed on 14 family members, seven of whom had detailed ophthalmic examinations. Medical history, ocular history and evaluation, visual field testing, full-field electroretinogram (ERG), and Whole Exome Sequencing (WES) results were analyzed. Three family members were homozygous for c.205_208dupCAGG;p.(Asp70Alafs*148) inAIREand homozygous for c.481-1G>A inPDE6C. One additional family member was homozygous for only theAIREvariant and another additional family member was homozygous for only thePDE6Cvariant. All patients with homozygosity for thePDE6Cvariant had cone dystrophy, and all patients with homozygosity for theAIREvariant had APS1. In addition, two of the family members who were homozygous for thePDE6CandAIREvariants had reduced rod function on ERG. We report the co-inheritance forAPS1andPDE6C-related cone dystrophy, an unusual example of two seemingly independent recessive conditions coinciding within a family. Dual molecular diagnosis must be taken into account by ophthalmologists facing unusual constellations of findings, especially in consanguineous families.