Hypotrichosis is a rare form of progressive hair loss characterized by sparse and occasionally woolly hair that is curly and breaks easily. Disease-causing mutations in LIPH, LPAR6 and KRT74 have recently been identified. We describe a four-generation pedigree from Turkey following an autosomal recessive pattern, in which the four affected members had hypotrichosis and woolly hair. By sequencing LPAR6 and the use of SNP arrays, we revealed a homozygous loss of the entire LPAR6 gene in the affected individuals. We hypothesize that the 12-kb deletion resulted from illegitimate recombination secondary to slip-replication. The orientation of three Alu repeats around LPAR6 may have provoked the formation of a triple-barrel structure during replication, thereby allowing strand slipping. This first report of complete LPAR6 loss expands the spectrum of known LPAR6 mutations and suggests a novel mechanism for this gene and for the formation of DNA rearrangements in general.