This review is organized as follows. Firstly, the principles of MEG, including the methods used to estimate brain activity and its relevance to neuronal oscillations, will be revised. Secondly, an extensive review of the methods commonly used to assess functional connectivity will be presented, in which the different methods are classified as undirected or directed according to their outputs, univariate or multivariate, and same-frequency or cross-frequency according to their inputs. Finally, the use of phase coupling methods on MEG data in the context of resting state, visuospatial attention and working memory will be presented. Table 1 clarifies the terminology used throughout this review.