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I've spent some time to deal with WCF securing with certificates and came to a solution that I want to share.
As you probably know, WCF supports certificate authentication and it's not so hard to set up. However you will need to install certificates on both the service machine and the caller machine. This can be a problem if you want to host the service on a shared hosting environment for example. Even if the service is hosted on a machine in your network you will still need some permissions to be given to the service application pool user in order to access the certificate private key.
Securing WCF Service with Self Signed Certificates programmatically - CodeProject