Cerebrotendinous xanthomatosis (CTX) is an autosomal recessive lipid storage disorder caused by pathogenic variants in the CYP27A1 gene, which encodes the mitochondrial enzyme sterol 27-hydroxylase. CTX is likely to be underdiagnosed and precise epidemiological characteristics are largely unknown. We conducted a nationwide survey on CTX to elucidate the frequency, clinical picture, and molecular biological background of Japanese CTX patients. Forty patients with CTX (50.0% male) were identified between September 2012 and August 2015. The mean age of onset was 24.5 ± 13.6 years, mean age at diagnosis was 41.0 ± 11.6 years, and corresponding mean duration of illness from onset to diagnosis was 16.5 ± 13.5 years. The duration of illness from onset to diagnosis was significantly longer in patients whose signs or symptoms appeared before the age of 15 (mean ± SD: 27.1 ± 16.8 years) than in those whose signs or symptoms manifested at 15 years or older (mean ± SD: 12.4 ± 9.6 years). At the time of the survey, the most common sign or symptom was tendon xanthoma, followed by intellectual disability/cognitive impairment, spastic paraplegia, juvenile cataract, cerebellar ataxia, sensory disturbance attributed to spinal cord, coronary artery disease, chronic diarrhea, parkinsonism/dystonia, peripheral neuropathy, epilepsy, and juvenile osteoporosis. The most predominant pathogenic variants in the CYP27A1 gene were c.1214G>A (p.R405Q, 31.6%), c.1421G>A (p.R474Q, 26.3%), and c.435G>T (p.G145=, 15.8%). Our survey revealed possible associations between p.R474Q and the classical form of CTX, p.R405Q and the spinal form of CTX, and c.435G>T and the non-neurological form of CTX. Therapeutic interventions that included single agent or combination of chenodeoxycholic acid (CDCA), HMG-CoA reductase inhibitor, and/or LDL apheresis reduced serum cholestanol level in all patients and improved clinical symptoms in 40.5% of patients. Although CTX is a treatable neurodegenerative disorder, our nationwide survey revealed a notable diagnostic delay, particularly among pediatric patients.