Many functionally important membrane proteins are cleaved within their transmembrane helices to become activated. This unusual reaction is catalyzed by a group of highly specialized and membrane-bound proteases. Here I briefly summarize current knowledge about their structure and mechanism, with a focus on the rhomboid family. It has now become clear that rhomboid protease can cleave substrates not only within transmembrane domains, but also in the solvent-exposed juxtamembrane region. This dual specificity seems possible because the protease active site is positioned in a shallow pocket that can directly open to aqueous solution through the movement of a flexible capping loop. The narrow membrane-spanning region of the protease suggests a possible mechanism for accessing scissile bonds that are located near the end of substrate transmembrane helices. Similar principles may apply to the metalloprotease family, where a crystal structure has also become available. Although how the GxGD proteases work is still less clear, recent results indicate that presenilin also appears to clip substrate from the end of transmembrane helices.