Autosomal recessive hypotrichosis (ARH) is characterized by sparse hair on the scalp without other abnormalities. Three genes, DSG4, LIPH, and LPAR6 (P2RY5), have been reported to underlie ARH. We performed a mutation search for the three candidate genes in five independent Japanese ARH families and identified two LIPH mutations: c.736T>A (p.Cys246Ser) in all five families, and c.742C>A (p.His248Asn) in four of the five families. Out of 200 unrelated control alleles, we detected c.736T>A in three alleles and c.742C>A in one allele. Haplotype analysis revealed each of the two mutant alleles is derived from a respective founder. These results suggest the LIPH mutations are prevalent founder mutations for ARH in the Japanese population. LIPH encodes PA-PLA1α (LIPH), a membrane-associated phosphatidic acid-preferring phospholipase A1α. Two residues, altered by these mutations, are conserved among PA-PLA1α of diverse species. Cys246 forms intramolecular disulfide bonds on the lid domain, a crucial structure for substrate recognition, and His248 is one amino acid of the catalytic triad. Both p.Cys246Ser- and p.His248Asn-PA-PLA1α mutants showed complete abolition of hydrolytic activity and had no P2Y5 activation ability. These results suggest defective activation of P2Y5 due to reduced 2-acyl lysophosphatidic acid production by the mutant PA-PLA1α is involved in the pathogenesis of ARH. Hum Mutat 31:1–9, 2010. © 2010 Wiley-Liss, Inc.