Structural Equation Models (SEM) is among of the most extensively applied statistical techniques in the study of human behavior in the fields of Neuroscience and Cognitive Neuroscience. This paper reviews the application of SEM to estimate functional and effective connectivity models in work published since 2001. The articles analyzed were compiled from Journal Citation Reports, PsycInfo, Pubmed, and Scopus, after searching with the following keywords: fMRI, SEMs, and Connectivity. Results: A 100 papers were found, of which 25 were rejected due to a lack of sufficient data on basic aspects of the construction of SEM. The other 75 were included and contained a total of 160 models to analyze, since most papers included more than one model. The analysis of the explained variance (R2) of each model yields an effect of the type of design used, the type of population studied, the type of study, the existence of recursive effects in the model, and the number of paths defined in the model. Along with these comments, a series of recommendations are included for the use of SEM to estimate of functional and effective connectivity models.