MIIS has its origins in two Canadian companies' products, Linkage Software's meta-directory product Link-Age Directory Exchange (LDE) which Microsoft acquired on June 30, 1997 and Zoom-it Corporation's meta-directory product, Via, which Microsoft acquired on July 7, 1999.

LDE was strongly email system oriented but traces of it and its field mapping technology remain through MIIS 2003.

After acquiring Zoom-it Via Microsoft renamed it to MMS (Microsoft Meta-directory Services) and offered this product for free; however they will strongly encourage customers to hire Microsoft Consulting Services to install and configure product.

Microsoft Identity Integration Server 2003 was completely re-written from ground up. No original Zoom-it Via code was moved into MIIS. However Microsoft preserved methodology and original idea of the Via product. MIIS 2003 no longer uses Z Script (proprietary scripting language of Zoom-it Via), instead it offered .NET framework support. With this upgrade Microsoft did not offer a migration path from MMS to MIIS due to the significant differences in the products.

Currently Service Pack 2 is available for MIIS 2003.

IIFP is a slimmed-down version of MIIS that is limited to synchronization between AD, ADAM, and exchange data-stores.

MIIS 2003 was recently (Fall 2007) incorporated into a new offering called Identity Life-cycle Manager 2007. This product was announced at the RSA Conference in February 2007 and made available to customers in May 2007. Identity Life-cycle Manager 2007 includes not only the original MIIS 2003 product, but also a component called Certificate Life-cycle Manager (CLM) which is used to manage X.509 digital certificate and smart card issuance.