A system and method for processing message threads is provided. A plurality of messages, each comprising a message body, is grouped by conversation thread. The message bodies of the messages are compared. Each message recursively contained in at least one other message is identified as a near duplicate message. An attachment sequence is generated for at least part of each attachment associated with one or more of the messages. The attachment sequences associated with the near duplicate messages are compared. Each near duplicate message having an attachment sequence not matching the attachment sequence of any other near duplicate message is identified as a unique message.