This paper analyzes the relevance of logical lines of investigation, relevance that has been developed in the jurisprudence and doctrine of the organs of the Inter-American System of Human Rights and mainly in the prosecution and judgement of system crimes discussed within the framework of process of transitional justice. This analysis is made from the standpoint of international obligations of States and the special duties that arise for these in the context of massive, widespread and systematic human rights violations. This paper aims to show that using different logical lines of investigation as a tool is very useful, especially in contexts of serious human rights violations; contexts that are extensive to non-institutionalized regimes that then go through transitions to democracy or peace.