Finely regulated and orchestrated events occur during seed development and germination in different cell organelles (mitochondria, peroxisomes, plastids, vacuoles, endoplasmic reticulum, oil bodies and nuclei). Therefore, some of the ongoing investigations pass through sub-cellular organelle purifications for a deeper comprehension of these complex developmental processes. In seed biology, recent ambitious efforts in proteomics have been directed toward organelle isolation from seeds and high-throughput protein separation and identification by mass spectrometry at defined developmental stages. The construction of reference maps allowed identifying organellespecific proteins and the analyses of their variation(s) depending on both internal and external stimuli helped to decipher the extent to which these proteins play fundamental role in seed physiology. Here, we report organelle proteomics applied to the characterization of seed physiological processes, and compare these advances with studies from other plant tissues.