Embryonic stem cells are useful to study the functional aspects of lineage commitment. In this study, we report that using the Cre/loxP system provides a useful tool for studying multifunctional proteins that are involved in stem cell differentiation, such as calreticulin. Calreticulin is a chaperone and a major calcium buffer of the endoplasmic reticulum and it functions during both adipogenesis and cardiomyogenesis. We used both a tamoxifen-inducible and cardiomyocyte-specific alpha-myosin heavy chain promoter-driven Cre/loxP system to study cardiomyogenesis, and a tamoxifen-inducible ubiquitously expressed cytomegalovirus promoter-driven Cre/loxP system to study adipogenesis. Both Cre/loxP systems mimicked the results previously observed using the calreticulin-null stem cell systems. Our results indicate that the tamoxifen-inducible Cre/loxP system is an effective and reliable tool to use for gene ablation in studies on functional aspects of stem cell biology.