Rod and cone photoreceptors degenerate under a variety of pathologic conditions, including those caused by bright light exposure and a wide array of hereditary retinal diseases, such as retinitis pigmentosa (RP), macular degeneration (MD), and cone-rod dystrophies. Defects in a large number of genes are linked to inherited retinal degenerative disorders (see more information at http://www.sph.uth.tmc.edu/RetNet/disease.htm). These genes include those encoding phototransduction-related proteins, such as rhodopsin, subunits of cyclic nucleotide phosphodiesterase (PDE), and cyclic nucleotide-gated (CNG) channel subunits, as well as genes encoding photoreceptor outer segment structural proteins, such as peripherin/rds. Secondary, or nonautonomous photoreceptor degeneration occurs when a disease gene expressed specifically in one type of photoreceptor (e.g., rods) leads to loss of photoreceptors that do not express the disease gene. For example, RP arising from defects in the rod-specific PDE gene leads to secondary loss of cones. Death of cones after rod death in RP is a characteristic of secondary photoreceptor degeneration associated with disease progression, and is also found in other human photoreceptor degenerations. Indeed, cone degeneration secondary to rod death has been studied intensively in human RP patients and in animal models of RP.1–4 In contrast, our understanding of the impact of cone degeneration on rod function and survival is very limited. Though early reports suggested normal or nearly normal rod function in patients with cone degenerations, such as achromatopsia and cone dystrophy,5–7 several recent studies have reported reduced rod electroretinographic (ERG) responses and disrupted rod photoreceptor mosaic in such disorders,8–10 suggesting that secondary impairment of rod function and viability may be a common consequence of primary cone degeneration. CNG channels, which are localized to the plasma membrane of the outer segment of rods and cones, play a pivotal role in phototransduction. In darkness, rod CNG channels are activated by binding of cyclic guanosine monophosphate (cGMP), allowing a steady inward cation (Na+ and Ca2+) current. Light triggers a sequence of enzymatic reactions that leads to the hydrolysis of cGMP, resulting in CNG channel closure, reduction in the inward cation current, and membrane hyperpolarization.11–14 A similar transduction scheme exists in cones. However, the CNG channels of rods and cones are formed from different A and B subunits, leading to profound differences in cGMP sensitivity, Ca2+ permeation, and functional modulation.15,16 The rod CNG channel is formed from CNGA1 and CNGB1 subunits, while the cone CNG channel is formed from CNGA3 and CNGB3 subunits. Heterologous expression studies have shown that the A subunits are responsible for the ion-conducting activity of the channel, whereas the B subunits function as modulators. Mutations in the rod-specific CNGA1 and CNGB1 genes are associated with RP,17,18 while mutations in the cone-specific CNGA3 and CNGB3 genes are linked to achromatopsia, cone dystrophy, and some maculopathies.6,19 Indeed, over 70 disease-associated mutations have been identified in CNGA3 and CNGB3,6,19–21 and these mutations account for over 70% of achromatopsia patients.6,22–24 Achromatopsia is a devastating hereditary visual disorder characterized by reduced cone-mediated ERG responses, color blindness, visual acuity loss, pendular nystagmus, extreme light sensitivity, and daytime blindness. As the disease is primarily caused by mutations in CNG channel subunits, achromatopsia is often referred to as a “channelopathy.” Cone degeneration in patients with CNG channel deficiency has been documented by optical coherence tomography (OCT) studies.25–27 Loss of cone function and progressive cone degeneration also has been documented in CNGA3−/− and CNGB3−/− mouse models.28–30 The current studies were designed to explore the secondary effects of cone degeneration on rods by characterizing rod function, structural integrity and survival after loss of cones in CNGA3−/− mice, a model for human achromotopsia. CNGA3−/− mice have no detectable cone ERG responses and develop early-onset cone degeneration,28,29 which is detected as early as the second postnatal week, with complete loss of cones from the ventral retina after the third postnatal month.29 In this report, we show secondary, age-dependent effects on rod-driven electrophysiological function in CNGA3−/− mice. The scotopic ERG b-wave was reduced as early as 1 month, while a reduced ERG a-wave only appeared much later, at 9 months. We also show a reduced outer nuclear layer (ONL) thickness and reduced expression of rod-specific proteins in CNGA3−/− mice at 12 months. Cone terminals in the CNGA3−/− retina showed a progressive loss of neurochemical and ultrastructural integrity, accompanied by disorganized rod terminal ultrastructure by 12 months. The appearance of scotopic ERG b-wave defects before a-wave deficits, together with the progressive loss of neurochemical and ultrastructural integrity of cone photoreceptor terminals, suggest that compromised CNG channel function and phototransduction lead to early impairment of synaptic terminal function and structural integrity. Our findings also indicate that impaired cone function leads to deleterious secondary effects on rod function, structure, and survival.