An accurate DNA damage response pathway is critical for the repair of DNA double-strand breaks. Repair may occur by homologous recombination, of which many different sub-pathways have been identified. Some recombination pathways are conservative, meaning that the chromosome sequences are preserved, and others are non-conservative, leading to some alteration of the DNA sequence. We describe an in vivo genetic assay to study non-conservative intra-chromosomal deletions at regions of non-tandem direct repeats in  Schizosaccharomyces pombe . This assay can be used to study both spontaneous breaks arising during DNA replication and induced double-strand breaks created with the  S. cerevisiae  homothallic endonuclease ( HO ). The preliminary genetic validation of this assay shows that spontaneous breaks require  rad52 +   but not  rad51 +  , while induced breaks require both genes, in agreement with previous studies. This assay will be useful in the field of DNA damage repair for studying mechanisms of intra-chromosomal deletions.