The World Trade Organization (WTO) is an intergovernmental organizations dealing with the rules of trade between its members. According to theory and organizational norms, in principle, only sovereign states and the separate customs territories are eligible to have the full membership of the WTO and enjoy the legal rights and have obligations. In addition to the members, the WTO also allows non-state actors, particularly nongovernmental organizations (NGOs) whose international legal personality are not recognized, to participate in international trade with diverse paths in respect of WTO activities. By analyzing two cases about the Biotech Products Dispute and the AIDS Drugs in South Africa, this paper compares the participation of NGOs and Transnational Corporations (TNCs) in the WTO. It shows that in spite of the similarity of their nature—the transnational non-state actor—between NGOs and TNCs, the formal participation of the former in the WTO has far less influence than the informal participation of the latter. In other words, TNCs seems to have much more real influence over the WTO than NGOs. This research finding demonstrates that forms of participation or pure institutional participation do not guarantee non-state actors to exert their influence on the WTO. Conversely, what kind of power used by them and the relationship they established with members’ governments are the critical factors to explain whether NGOs really can make some differences in the WTO.