In Cre-loxP recombination system, Cre recombinase binds cooperatively to two 13 bp inverted repeats in a 34 bp loxP and catalyzes strand exchange in the 8 bp spacer region. Up to date, spacer sequences within the recombined loxP sites derived from two loxP sties that have different 8 bp spacer regions have never been analyzed. In the present study, we analyzed the spacer sequences within the recombined products, resulted from intramolecular recombination between heterologous loxP sites including M2, M3, M7, M11, and 2272 in vivo and in vitro. From the analyses, it was found that loxP sites with aberrant 8 bp spacers can be generated from Cre-mediated recombination between heterologous loxP sites at significantly high frequency, proposing the possibility that recombination between heterologous loxP sites would have not undergone typical formula of Cre-loxP recombination. (C) 2007 Elsevier Inc. All rights reserved.