Hatchling processing methods and systems that provide for the processing of hatchlings at a plurality of processing stations, with the hatchlings being transferred between stations using an automated conveying system. Each of the hatchlings is retained in a hatchling carrier designed to be conveyed by the automated conveying system. Each of the hatchling carriers is preferably designed to retain only one hatchling at a time. The systems and methods may also include identification tags that may be used to direct the hatchling through the processing system with the automated conveying system. The identification tags may be associated with the hatchlings themselves or they may be associated with the hatchling carriers.