Rod photoreceptor-specific mutations cause ectopic synapses to form between cone photoreceptor terminals and rod bipolar cell dendrites in degenerating retinas of rhodopsin transgenic (P347L) pigs and retinal degeneration mice. Since the mutations occur in rod photoreceptor-specific genes in these two models, it is not known if ectopic synaptogenesis occurs specifically due to some rod photoreceptor cell-autonomous properties of a mutation or as a general consequence of photoreceptor degeneration. In the Royal College of Surgeons (RCS) rat, a mutation in the receptor tyrosine kinase gene, Mertk, causes failure of the retinal pigment epithelial (RPE) cells to phagocytose shed photoreceptor outer segments; subsequently, both rod and cone photoreceptors die. The non-phagocytic phenotype of the RCS rat is RPE cell-autonomous and the photoreceptors degenerate secondarily. Here we show that in 35-day-old RCS rats, where a majority of rod and cone photoreceptors remained, rod bipolar cell dendrites had abnormal (flat-contact type) synaptic contacts with rod and cone terminals. Demonstration of ectopic synapses in the RCS rat suggested that ectopic synaptogenesis could occur as a result of photoreceptor degeneration, even when the rods and cones were developmentally normal. This further supported the hypothesis that ectopic synaptogenesis may be a common step in the disease progression of different forms of retinal degeneration that include photoreceptor death as a feature, such as retinitis pigmentosa.