We aimed to unravel the molecular genetic basis of inherited retinal degeneration (IRD) in a comprehensive cohort of patients diagnosed in the largest center for IRD in Germany. A cohort of 2,158 affected patients from 1,785 families diagnosed with IRD was analyzed by targeted next-generation sequencing (NGS). Patients with single-gene disorders (i.e. choroideremia, retinoschisis) were analyzed by Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). Our study cohort accounts for approximately 7% of the estimated 30,000 IRD patients in Germany, thereby providing representative data for both the prevalence of IRDs and the mutation spectrum of IRD genes for the population in Germany. We achieved a molecular diagnostic rate of 35%-95%, depending on the clinical entities, with a high detection rate for achromatopsia, retinoschisis and choroideremia, and a low detection rate for central areolar choroidal dystrophy and macular dystrophy. A total of 1,161 distinct variants were identified, including 501 novel variants, reaffirming the known vast genetic heterogeneity of IRD in a mainly outbred European population. Our study demonstrates the clinical utility of panel-based NGS in a large and highly heterogeneous cohort from an outbred population and for the first time gives a comprehensive representation of the genetic landscape of IRDs in Germany. Our data are valuable and crucial for the scientific community and health care providers, but also for the pharmaceutical industry in the progressing field of personalized medicine and gene therapy. This article is protected by copyright. All rights reserved.