The function of biological cells is intimately associated with their internal organization, in which multiple subcellular structures have specialized roles. Such subcellular structures hold the secrets to normal cellular function, progression of disease, and the universe of interactions among biomolecules that define life. Initially observed in unicellular organisms, these subcellular structures were termed organelles because of the parallel to the organ/body relationship in multicellular organisms. Currently, the term "organelle" loosely describes a confined subcellular environment of any cell in which specific functions occur. Thus, organelles comprise large protein complexes (e.g. signalosomes), large protein-RNA complexes (e.g. ribosomes), and membrane bound structures (e.g. mitochondria). The interest in subcellular organization continues to increase as new biological functions, unique molecular features, and therapeutic potential continue being discovered. This interest has fueled recent advances in the bioanalysis of organelles reviewed here. Because of their diversity in general architecture, taxonomical origin, and function, the approaches and methodologies to investigate organelles are not unique. From an analytical perspective, prokaryotic organelles, biomolecular complexes (membrane-less and non-membranous organelles) and membrane bound structures all require different strategies, which would be impossible to cover in a single review. Based on the relevance of membrane bound eukaryotic organelles in recent key biomedical discoveries, we focus this review on these organelle types (Table 1). They include: subcellular structures bound by a single lipid layer (e.g., lipid droplets), by single phospholipid bilayer (e.g., lysosomes) or a double phospholipid bilayer (e.g. autophagosomes); it also includes membranous structures with complex topologies (e.g., Golgi). This review excludes all prokaryotic organelles as well as eukaryotic membrane-less and non-membranous organelles. The interested reader on these organelle types will find several relevant references in Table 2. Table 1 Organelles covered in this review.