Objective: To analyze the clinical symptoms and hereditary information of suspicious juvenile neuronal ceroid-lipofuscinosis (JNCL) and determine the genotype in order to explore the diagnosis clues in the patients with ophthalmologic manifestations being initial symptom. Methods: A case-control study was performed in this study.Two families were included in Eye Hospital of Wenzhou Medical in 2013 and 2017, respectively.Medical histories were collected and all participants underwent comprehensive ophthalmologic examinations, and the best corrected visual acuity (BCVA) was obtained.Fundus photography and optical coherence tomography (OCT) were used to image the retinal signs, and visual electrophysiology was recorded to evaluate the visual function.Genomic DNA of 3 patients who initially visited to ophthalmologists and 5 unaffected family members were extracted.Whole exome sequencing (WES), targeted exome sequencing (TES), Sanger sequencing and comprehensive analyses of pathogenicity were performed to determine the genetic cause of the patients.This study was approved by Ethics Committee of Eye Hospital of Wenzhou Medical University (KYK-2017-7), and written informed consent was obtained from each subject prior to any medical examination. Results: All patients presented bull eye sign and disorder of pigment on the fundus photograph, and the retinas were thinning on the OCT image, indicating the diffuse retinal pigment epithelium atrophy of macula and loss of outer layer structure of retina.Three mutations in CLN3 gene were identified by WES, TES, Sanger validation and assessments of pathogenicity, including c. 154T>C(p.Y52H), c.982G>C(p.A328P) and c. 906+ 5G>A, among which p. A328P was a novel mutation.Patients of F1 family harbored the compound heterozygous mutations c. 154T>C (p.Y52H) and c. 982G>C(p.A328P), while proband of F2 family harbored the homozygous splice site mutation c. 906+ 5G>A, which was reported to be a pathogenic mutation of JNCL.Co-segregation and comprehensive pathogenicity analysis revealed that the compound heterozygous mutations in F1 family and the homozygous mutation in a splice site in F2 family were the genetic causes of their phenotypes. Conclusions A novel mutation in CLN3 gene for JNCL is identified, which expands the mutation spectrum of CLN3 gene.Considering the high clinical heterogeneity of inherited retinal diseases, especially syndromic cases, genetic test through next generation plays a vital role in diagnosis, guiding future treatment and prognostic evaluation.