Among various genetic causes of nephronophthisis (NPHP), a total homozygous deletion of NPHP1, NPHP type I (NPHP1), is the most common type manifesting with the isolated kidney involvement of typical juvenile NPHP in majority. Korean patients with a clinical diagnosis of NPHP (n = 57) were screened for total deletion of NPHP1, which revealed five patients with total deletion of NPHP1. Chronic renal failure was diagnosed in these patients at 7.9–15.4 years of age and all had a progressive decrease in visual acuity with various ages of onset (2–17 years). An ophthalmologic examination revealed retinopathy with large or small flecks, which was compatible with Stargardt disease or albipunctatus retinopathy in 4 of the 5 patients. No other organ involvement was observed. The genetic study revealed an additional deletion of exon 1 of MALL, a gene adjacent to NPHP1. We report the unexpectedly common retinal involvement of NPHP1 with an additional MALL deletion in Korean NPHP patients. While further study is necessary to verify this finding, retinal examinations are necessary for NPHP patients to search for retinal involvement, and in patients with retinopathy, screening for a homozygous deletion of NPHP1 should be considered for genetic diagnoses.