Methods to detect and analyze somatic mutations in higher organisms are critically important in view of their causal role in cancer, heritable diseases, and, possibly, aging. Here, we describe detailed protocols for the use of a mutational reporter system based on lacZ-containing plasmids integrated in the germline of Mus musculus and Drosophila melanogaster. Plasmids containing the bacterial lacZ gene integrated at one or more chromosomal sites can be excised, purified and recovered in suitable Escherichia coli hosts allowing the positive selection of mutant lacZ genes and their further molecular characterization. This system is capable of detecting a broad range of mutational events, varying from small mutations in the lacZ reporter gene to large genome rearrangements with one breakpoint in lacZ and the other breakpoint elsewhere in the genome.