A cDNA clone of the rat sucrase-isomaltase (SI) structural gene detected two distinct patterns of DNA fragments on Southern blots of mouse DNA. Screening of 18 AKXL and 25 AKXD recombinant inbred (RI) strains revealed that all bands in each pattern co-segregated and there were no (0/43) recombinants with Es-26 on mouse Chromosome (Chr) 3. Since CBA/CaJ mice have approximately threefold less sucrase activity than other strains, we intercrossed them with SJL/J mice to map the previously identified SI regulatory gene, Si-r. Fifty-six mice from the F2 generation were assayed for sucrase activity, and the genotype of the murine SI structural gene locus, Si-s, was determined by Southern blot analysis. Nine animals (16%) were homozygous for the CBA/CaJ allele (C) and had an average sucrase activity (jejunum+ileum) of 1.51 mumoles/h/mg protein (SE = 0.067), 19 (34%) were homozygous for the SJL/J allele (S) and had an average sucrase activity of 5.95 mumoles/h/mg protein (SE = 0.267), and 28 (50%) were heterozygous (C/S) for Si-s with an average sucrase activity of 3.70 mumoles/h/mg protein (SE = 0.127). We conclude that Si-s and Si-r are closely linked on Chr 3.