This article discusses the use of X.509 certificates in Federation metadata. It has security implications so please read it carefully.
A SAML entity uses public key cryptography to secure the data transmitted to trusted partners. Public keys are published in the form of X.509 certificates in metadata whereas the corresponding private keys are held securely by the entity. These keys are used for message-level signing and encryption, and to create secure back channels for transporting SAML messages over TLS. They are not used for browser-facing TLS transactions on port 443. See the Key Usage topic for more information.
Certificates in metadata are used for message-level signing and encryption, not browser-facing TLS transactions on port 443.
The InCommon Federation is based on the Explicit Key Trust Model, one of several possible metadata trust models. Consequently, the use of long-lived, self-signed certificates in metadata is strongly recommended. Certificates signed by a Certification Authority (CA) are allowed, and in most situations will work just fine, but the use of certificates other than self-signed certificates is discouraged. See the Background information and the Interoperability notes below for further discussion.
From a security perspective, the only element of a certificate in metadata that matters is the public key. Conforming software will ignore all other certificate content.
Any certificates you want to use with your SAML software are uploaded via the Federation Manager. Typically only one certificate is required per entity but multiple certificates may be uploaded and used as needed. In particular, multiple certificates may be used to facilitate the controlled rollover of expired certificates or compromised keys. To avoid interoperability problems, refer to the Certificate Migration topic for recommended guidelines regarding the rollover process.
It is easy to create a self-signed certificate with the OpenSSL command-line tool. Before you do this, however, take a moment to consider how best to handle the all-important private key.
Before generating a new private signing key for your IdP, read the IdP Key Handling topic.
In the base SAML metadata specification , a certificate signing authority (CA) has no assumed relevance to the trust model that secures the interactions among a federation's participants. In fact, certificates signed by a CA are discouraged since they can create interoperability issues in certain situations and lead to configurations that mistakenly establish trust based on the certificate signer. Allowing self-signed certificates simplifies the work of participants who may be required to join multiple federations, or who support local systems that are not registered in the Federation.
InCommon conforms to the SAML V2.0 Metadata Interoperability Profile  from OASIS. Participant site administrators securely transmit X.509 certificates and metadata to InCommon via the administrative web interface. InCommon signs the entire metadata file, securing the keys of its participants whether those keys are bound to self-signed certificates or certificates signed by a CA. The critical element in the certificate is the public key, which is associated with an entity via its entity ID. Theoretically, if all the relevant software systems could accept a public key without a certificate wrapper, InCommon would only need to include the public key of each entity. As it is, the certificate is a convenient container for the public key, the critical element being that the key is bound to a particular entity in the metadata.
InCommon sets the following security and trust requirements around certificates included in Federation metadata:
Consider the following interoperability issues as you set up and maintain your deployment:
<md:EntityDescriptor>element containing more than one encryption key.
 Metadata for the OASIS Security Assertion Markup Language (SAML) V2.0 http://saml.xml.org/saml-specifications
 SAML V2.0 Metadata Interoperability Profile http://wiki.oasis-open.org/security/SAML2MetadataIOP
 X.509 Certificates in the Federation Metadata: A technical webinar presented by the InCommon Technical Advisory Committee (October 22, 2009)
 The Shibboleth ExplicitKey Trust Engine https://wiki.shibboleth.net/confluence/display/SHIB2/ExplicitKeyTrustEngine
]5] Shibboleth Security and Networking https://wiki.shibboleth.net/confluence/x/VoEOAQ