The approval of methodologies involving the transportation sector confronts methodological concepts that hinder the eligibility of such projects as Clean Development Mechanism, mainly because it is a segment whose emissions come from mobile sources. The verification of additionality and monitoring of emissions, in principle, can be regarded as some of the key barriers to fit transportation sector projects into the CDM framework. This paper discusses these issues and examines, in particular, the road-rail intermodality. Since the partial replacement of cargo transport via trucks by wagon trains presents a great potential for mitigating emissions of greenhouse gases, this paper also analyzes the characteristics that a project involving road-rail intermodality must possess in order to be approved by the Executive Board of the United Nations Framework Convention on Climate Change. It also analyzes the main difficulties that such a project might face.