The structure of EDI messages is a recursive (embedded) structure, standardised at several levels. When creating messages those involved in the standardisation project reviewed which data could possibly occur in a given document and at which levels of message organisation. This review resulted in a so-called “super-set” of data, whose elements could be organised into a previously standardised recursive structure. Actual EDI connections generally use a partial set of the data super-set, the so-called data sub-set. However, the position of sub-set data is pre-defined in the standard of the message structure. This way instead of having to reconcile the message structures (as has to be done with schemes in the case of XML, for example), only the data found in the sub-set have to be compared. The data reconciliation phase of EDI development concerns this data comparison at sub-set level. EDI also uses standard documents, the so-called Message Implementation Guidelines (MIGs) for data reconciliation, which constitute the second range of documents mentioned under the planning of EDI. Manufacturers or buyers use these documents to inform their suppliers of the data they wish to use in connection with a specific EDI message document.

EANCOM standards are frequently used during data reconciliation. These are the standards used within a given EDI circle for the sub-set of a given message type, for example an invoice. In Hungary an EANCOM standard applies to invoice messages of the commercial circle of EDI users.

What is important for companies from the above is that their own business management systems must be capable of processing the data of the sub-set when receiving messages and generating them for messages to be sent. For this purpose data and file format reconciliation must be performed between the service provider and the system administrator of the company. In most cases the internal or export-import file format used by the company is chosen as the standard file format.