In the World Trade Organization (WTO) jurisprudence, the Appellate Body (AB) has repeatedly affirmed that WTO Members have the prerogative right in setting any level of protection that they deem appropriate (ALOP). At the same time, WTO Agreements provide for disciplines that a WTO Member must respect when it selects regulatory measures to fulfill its ALOP. Thus, a WTO Member’s autonomy in setting its ALOP, on the one hand, and the full force of other disciplines, on the other hand, are in a constant state of tension. Then, exactly how does a panel balance a Member’s right of setting its ALOP with a myriad of other trade obligations? To what extent is this right respected in the WTO dispute settlement processes? This article argues that the case law has confirmed that a Member’s obligations under the WTO Agreement on the Application of Sanitary and Phytosanitary Measures (SPS Agreement) must be read in light of the Member’s chosen ALOP, and that the AB has also demonstrated sensitivity and deference to a Member’s ALOP under the SPS Agreement. The same conclusion, however, cannot be easily applied to Article XX of the General Agreement on Tariffs and Trade 1994 (GATT 1994). Indeed, the case law under Article XX has demonstrated inconsistencies as to when WTO Members’ right to set their ALOP will be respected. I argue that such inconsistencies may be explained by a value-based, pragmatic approach adopted by the AB.