We have constructed shuttle vectors for integration of genes via double homologous recombination into three ectopic sites on the chromosome of Bacillus subtilis. The sites of integration are the pyrD, gltA, and sacA genes located at 139degrees, 172degrees, and 333degrees, respectively, on the chromosome. Integration of the vectors into the target genes leads to antibiotic resistance as well as different metabolic phenotypes. B. subtilis strains with integrations of the empty vectors were able to sporulate at rates comparable to wild type cells. Similar levels of expression were obtained from constitutive lacZ fusions integrated at the different sites. (C) 2004 Elsevier Inc. All rights reserved.