The purpose of this article is to analyze the relationship between trade unions and political parties based on the internal dynamics developed in the Central Unitaria de Trabajadores (CUT) during the first years of the reconstituted CUT, considering the period between its foundation in August 1988 and the celebration of the Refoundational Congress in 2003 as the time of study. In this sense, we argue that the conflicts experienced by the CUT would represent a good example of the problems generated by the close relations between political parties and union leaders, controversies that would call into question the concepts of autonomy and political dependence between both actors, an issue where the character of the union project(s) represented in the unitary central and its possibilities of influencing the Chilean political process were at stake. Thus, based on the analysis of periodical sources and interviews with union leaders, we seek to develop new lines of research to explain the union trajectory in the 1990s and the problems and challenges of the union movement in a period of great global transformations.