We have determined the molecular genetic basis of the rat beige mutant, a model for human Chediak-Higashi syndrome. Deletion of a 578-bp sequence, which led to a frame shift and a presumably non-functional truncated BEIGE protein, was identified in beige cDNA. The beige rat had a deletion of about 20 kb of genomic DNA, including three exons, which constitute the deleted 578-bp cDNA fragment. LINE1s (Long Interspersed Nucleolar Element 1) were identified at the site of the deletion. Consensus recognition sequences for DNA topoisomerase I were clustered at the putative deletion junction sites in LINE1s. We conclude that the deletion in the beige gene mediated by recombination between LINE1s is the causative mutation in the beige rat. The recombination might have been induced by DNA topoisomerase I and the extensive sequence homology between LINE1s.