Protocol encryption (PE), message stream encryption (MSE) or protocol header encrypt (PHE) are related features of some peer-to-peer file-sharing clients, including BitTorrent clients. They attempt to enhance privacy and confidentiality. In addition, they attempt to make traffic harder to identify by third parties including internet service providers (ISPs). However, encryption will not protect one from DMCA notices from sharing not legal content, as one is still uploading material and the monitoring firms can merely connect to the swarm.

MSE/PE is implemented in BitComet, BitTornado, Deluge, Flashget, KTorrent, libtorrent (used by various BitTorrent clients, including qBittorrent), Mainline, μTorrent, qBittorrent, rTorrent, Transmission, Tixati and Vuze. PHE was implemented in old versions of BitComet. Similar protocol obfuscation is supported in up-to-date versions of some other (non-BitTorrent) systems including eMule.