Calibration of holographic data storage systems (HDSS) is provided by utilizing holographic media (4) having calibration features which can be read, written, or read and written by a HDSS (30). Calibration features may represent for example, surface-relief gratings, holographic recordings, amplitude varying regions, or magnetic regions, or a combination thereof, at locations on or within the media. One or more of the calibration features along media region (302) are media calibration features with media and format information, and other calibration features along region (301) are system calibration features for optically and mechanically aligning HDSS optics. The media (4) may have performance calibration features along region (307) which can be recorded by a HDSS and then read back to determine characteristics of the media. Different HDSS systems can read the calibration features of the media (4) when installed in each HDSS to obtain information about the media, and to optically and mechanically align the media for optimal operation with the media.