Type 1 nephronophthisis (NPHP) with homozygous deletions of nephrocystin [NPHP1, DEL] has been considered a pure renal disorder, but co-occurrence of extrarenal symptoms, mainly retinitis pigmentosa, is observed in a subset of patients. Recently, [NPHP1, DEL] has been detected in three patients with Joubert syndrome-related disorders (JSRDs), who associated neurological signs with a peculiar neuroradiological malformation known as the 'molar tooth sign' (MTS). To define the frequency of JSRD spectrum in NPHP1 patients, we re-examined 56 cases with [NPHP1, DEL] and found an overall incidence of 8.9% (five out 56 patients). All had small hyperechoic kidneys and had developed advanced renal failure within 15 years. Two patients presented the complete features of JSRD with cerebello-renal-retinal association and MTS. Two others showed, instead, severe intentional tremor and thick superior cerebellar peduncles on brain magnetic resonance imaging (MRI), and one of them had associated retinopathy. The fifth patient presented with hypotonia, developmental delay, central deafness, and ataxia associated with Leber congenital amaurosis and liver fibrosis but with normal brain MRI. Marked intrafamilial variability of associated extrarenal symptoms was observed in familial cases. Deletion extension did not differ in patients with isolated renal phenotype and in those with associated neurological symptoms. In conclusion, neurological defects varying from subtle involvement of cerebellum with thickened peduncle to both JSRD and diffuse central hypotonia are frequent in [NPHP1, DEL] patients. Prevalence of such association may justify systematic neurological and neuroradiological evaluation.