To perform thread-based message prioritization, metadata may be extracted from a received electronic message. Based on the extracted message metadata and accumulated metadata extracted from previously received messages, a message thread to which the received electronic message belongs may be identified. Based on a set of thread priority assessment criteria, a priority level for the message thread may be determined. At least part of the message thread may be processed according to the priority level. The processing may be altering a notification behavior of an electronic messaging client for electronic messages of the message thread. Thread priority assessment may be based on user-configurable criteria that may be set via a graphical user interface. Message thread identification may also be based on user-configurable criteria that may be set via a graphical user interface.