Scleraxis (Scx) is a basic helix-loop-helix transcription factor that is a marker for the tendon/ligament cell lineage. The ∼11 kb genomic region from the mouse Scx gene locus faithfully recapitulates the endogenous Scx expression pattern in ScxGFP transgenic (Tg) mice. We have established two Tg mouse lines expressing Cre-recombinase (Cre) using this regulatory region (ScxCre-L and ScxCre-H). The specificity and efficiency of Cre recombination in these Tg lines are evaluated by crossing with Rosa-CAG-LSL-tdTomato (Ai14) or ROSA26R (R26R) reporter mice. The recombination in ScxCre-H;Ai14 mice is efficiently achieved in the endogenous Scx expression domains including the branchial arches, the syndetome, and the lateral plate mesoderm. Further analysis of ScxCre-H;Ai14;ScxGFP embryos reveal that expression of the ScxGFP transgene largely overlaps with Cre activity detected by tdTomato at embryonic day 12.5 (E12.5). In ScxCre-L;R26R or ScxCre-H;R26R neonates, Cre activity is detected in tendons, ligaments, intervertebral discs, joints, and cartilage around the chondro-tendinous/ligamentous junction, the prospective enthesis. The present results suggest that ScxCre Tg lines are useful for targeting the gene specifically in the Scx-expressing domains. genesis 51:275–283. © 2013 Wiley Periodicals, Inc.