An egg transfer system for providing automated inspection and tracking of eggs prior to entering an egg breaker, as well as broken egg contents following breaking, and in which the transfer system includes a series of processing and inspection component interfacing with a central processor for grading and segregating the eggs into one of a number of classes including removal eggs. Removal gates are provided at intermediate locations of the egg transfer system, prior to the egg breakers, and are associated with removal of varying classes of eggs. The central processor interfaces with the various stations in order to assemble a dedicated data packet of egg related data which is assigned to a progressing location on the egg conveyor upon which a specified egg is located, and which can further include the central processor assigning the data packet to a location subsequent to the breakers holding specified shell egg contents. At least one, and typically two, manual removal locations are additionally provided, such as associated with the intermediate egg detection and removal station as well as the post-breaker station.