Fundus autofluorescence is a valuable imaging tool in the diagnosis of inherited retinal dystrophies. With the advent of gene therapy and the numerous ongoing clinical trials for inherited retinal degenerations, quantifiable and reliable outcome measurements continually need to be identified. In this retrospective analysis, normalized and non-normalized short-wavelength (SW-AF) and near-infrared (NIR-AF) autofluorescence images of ten patients with mutations in visual cycle (VC) genes and nineteen patients with mutations in phototransduction (PT) genes were analyzed. Normalized SW-AF and NIR-AF images appeared darker in all patients with mutations in the VC as compared to patients with mutations in PT despite the use of significantly higher detector settings for image acquisition in the former group. These findings were corroborated by quantitative analysis of non-normalized SW-AF and NIR-AF images; signal intensities were significantly lower in all patients with mutations in VC genes as compared to those with mutations in PT genes. We conclude that qualitative and quantitative SW-AF and NIR-AF images can serve as biomarkers of deficiencies specific to the VC. Additionally, quantitative autofluorescence may have potential for use as an outcome measurement to detect VC activity in conjunction with future therapies for patients with mutations in the VC.