After genetically modified organisms and nanotechnology, EU food regulators are currently facing the challenge of choosing an appropriate policy approach towards animal cloning for food supply. While different regulatory options are being discussed, the ultimate choice of the EU is likely to have ramifications for EU’s compliance with the international legal trade order of the WTO. In this paper I take the EU policy debate as a starting point to outline the main legal issues that future EU regulation on animal cloning could raise with regard to the most pertinent WTO Agreements, the GATT, the SPS Agreement, and the TBT Agreement. I argue that any future legal assessment of EU policy in this area should pay particular attention to the thorough delineation between the scopes of application of these agreements, since the choice of the applicable WTO regime will directly impact on the extent to which the EU enjoys regulatory autonomy to pursue its policy choice. In the light of the recent Panel report in EC-Biotech the applicability of the SPS Agreement also to future EU measures on animal cloning appears likely thereby resulting in strong constraints on EU policy choice. This appears problematic seeing that strong criticism is voiced against the extensive interpretation of the concept of an SPS measure, as undertaken by the Panel in EC-Biotech; and that doubts persist as to whether potential risks related to animal cloning can, in fact, be characterized as sanitary and phytosanitary risks.