The secretome, or secretomics, has recently emerged as a new term to describe the global study of proteins that are secreted by a cell, tissue or organism at any given time or under certain conditions. The secretome constitutes an important class of proteins that control and regulate a multitude of biological and physiological processes, thus making it a clinically relevant source for biomarkers and therapeutic target discoveries. There are several approaches that are being implemented to study such a class of proteins; however, each of these approaches has its advantages and limitations. While genome-wide studies using signal predictions can provide a comprehensive analysis of the secretome, the detection and quantification of the actual secreted proteins in a tissue would be more relevant. The goal of this review is to provide an overview of the methods currently used to analyze such a class of proteins, as well as the challenges encountered during the study of the secretome. The implication of studying the cell secretome together with its clinical relevance will be also covered.