Economic geologists have studied the Cu contents of biotite for at least a quarter of a century as potential guides for exploration and as clues to the genesis of porphyry copper deposits1–12. These earlier studies used bulk analytical techniques, and a common, although cautious, assumption was that Cu substituted for Fe in the octahedral sites of the biotite. Here we report data from high-resolution and X-ray analytical transmission electron microscopy which demonstrate that anomalous Cu in biotite is present primarily as submicrometre inclusions of pure native Cu in the interlayer regions of the mica. The inclusions occur with greatest density and size in mixed-layer sheet silicate domains which form by alteration of biotite and chlorite. Less abundant and smaller Cu inclusions are associated with biotites that show subtle alteration only on the high-resolution transmission electron microscopy scale. The association of Cu inclusions with alteration domains, coupled with mass-balance considerations, suggests that these sheet silicates act as Cu sinks, and not as sources for primary mineralization.