beta-Galactosidase (beta-gal) is one of the popular reporters for detecting the expression of endogenous or exogenous genes. Here we report 6-chloro-3-indoxyl-beta-D-galactopyranoside (S-gal) is more sensitive for beta-gal activity than 5-bromo-4-chloro-3-indolyl-beta-D-galactoside (X-gal), particularly during the early developmental stages of mouse embryos. Further, we successfully combined beta-gal staining with S-gal and in situ hybridization using DIG-labeled probes in both whole and sections of early stage embryos due to the sensitivity and color compatibility of S-gal.