The present invention relates to organisms which are homozygous for targeted modification of one or more endogenous genes. More specifically, the invention concerns organisms (e.g., plants or animals) in which both alleles of a gene are disrupted but in which the homozygous knockout organism does not contain exogenous sequences at the disrupted locus. The invention also concerns organisms (e.g., plants or animals) in which both alleles of a gene are modified by insertion of a transgene, wherein the transgene lacks sequences encoding a reporter (e.g., selectable marker).