Replication Protocols used with Active Directory

Active Directory requires a network protocol for replication traffic. Within a single site, only one protocol is used for replication. In a multiple site structure, you must select a replication protocol for replication between sites.

Active Directory replication uses Remote Procedure Call (RPC) over IP for replication within a site. RPC is an industry standard protocol for client/server communications that is compatible with most types of networks. For replication within a site, RPC provides uniform, high-speed connectivity.

When you configure replication between sites, you have a choice of replication protocol. You must choose between RPC over IP^[1] or the Simple Mail Transfer Protocol (SMTP)^[2].
A note about SMTP SMTP is used to send mail on the Internet. SMTP is a more reliable transport, but it requires more network overhead. Because we establish sites to conserve bandwidth, using SMTP defeats this purpose. The only good reason to use SMTP would be if you are experiencing dropped connections with RPC.
SMTP has one restriction: you can use it only for replication between domain controllers in different domains. In most cases, choose RPC over IP for replication between sites.
Active Directory Sites and Services labels the protocol for connections within a site as RCP and the protocol for connections between sites as IP. Both labels, however, mean that the connection uses RPC over IP. The only good reason to use SMTP would be if you are experiencing dropped connections with RPC. The Slide Show below describes the replication protocols for intra and inter-site replication.

[1]RPC over IP: Remote Procedure Call is a message-passing facility that is used for remote administration of computers. It can run over the Internet Protocol

[2] SMTP: Simple Mail Transfer Protocol; a protocol often used for sending Internet mail, which can also be used for replication over site links in Active Directory.