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Mediation analysis is routinely adopted by researchers from a wide range of applied disciplines as a statistical tool to disentangle the causal pathways by which an exposure or treatment affects an outcome. The counterfactual framework provides a language for clearly defining path-specific effects of interest and has fostered a principled extension of mediation analysis beyond the context of linear models. This paper describes medflex, an R package that implements some recent developments in mediation analysis embedded within the counterfactual framework. The medflex package offers a set of ready-made functions for fitting natural effect models, a novel class of causal models which directly parameterize the path-specific effects of interest, thereby adding flexibility to existing software packages for mediation analysis, in particular with respect to hypothesis testing and parsimony. In this paper, we give a comprehensive overview of the functionalities of the medflex package.