Autosomal recessive Stargardt macular dystrophy is caused by mutations in the photoreceptor disc rim protein ABCA4/ABCR. Key clinical features of Stargardt disease include relatively mild rod defects such as delayed dark adaptation, coupled with severe cone defects reflected in macular atrophy and central vision loss. In spite of this clinical divergence, there has been no biochemical study of the effects of ABCA4 deficiency on cones vs. rods. Here we utilize the cone-dominant Abca4^−/−/Nrl^−/− double knockout mouse to study this issue. We show that as early as post-natal day (P) 30, Abca4^−/−/Nrl^−/− retinas have significantly fewer rosettes than Abca4^+/+/Nrl^−/− retinas, a phenotype often associated with accelerated degeneration. Abca4-deficient mice in both the wild-type and cone-dominant background accumulate more of the toxic bisretinoid A2E than their ABCA4-competent counterparts, but Abca4^−/−/Nrl^−/− eyes generate significantly more A2E per mole of 11-cis-retinal (11-cisRAL) than Abca4^−/− eyes. At P120, Abca4^−/−/Nrl^−/− produced 340±121 pmoles A2E/nmol 11-cisRAL while Abca4^−/− produced 50.4±8.05 pmoles A2E/nmol 11-cisRAL. Nevertheless, the retinal pigment epithelium (RPE) of Abca4^−/−/Nrl^−/− eyes exhibits fewer lipofuscin granules than the RPE of Abca4^−/− eyes; at P120: Abca4^−/−/Nrl^−/− exhibit 0.045±0.013lipofuscingranules/μm² of RPE vs. Abca4^−/− 0.17±0.030lipofuscingranules/μm² of RPE. These data indicate that ABCA4-deficient cones simultaneously generate more A2E than rods and are less able to effectively clear it, and suggest that primary cone toxicity may contribute to Stargardt's-associated macular vision loss in addition to cone death secondary to RPE atrophy.