Purpose: To identify the genetic defect in a three-generation Chinese family with congenital cataracts. Methods: The phenotype of a three-generation Chinese family with congenital cataract was recruited. Detailed family history and clinical data of the family were recorded. Candidate genes sequencing was performed to screen out the disease-causing mutation. Bioinformatics analysis was performed to predict the function of mutant gene. Results: The phenotype of the family was identified as nuclear cataract. Direct sequencing revealed a c.161 G>T transversion in exon 1 of crystallin alpha-A (CRYAA). This mutation co-segregated with all affected individuals in the family and was not found in unaffected family members nor in the 100 unrelated controls. Bioinformatics analysis indicated that the 54th amino acid position was highly conserved and the mutation R54L caused an increase of local hydrophobicity around the substitution site. Conclusions: This study identified a novel disease-causing mutation c.161 G>T (p. R54L) in CRYAA in a Chinese family with autosomal dominant nuclear cataracts, this is the first report relating a G>T mutation in CRYAA leading to congenital nuclear cataract.