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Three-dimensional images of crustal seismic structure beneath the East Pacific Rise show pronounced axial heterogeneity over distances of a few kilometres. A linear high-velocity anomaly, approximately 1–2 km in width and restricted to the uppermost 1 km of the crust, is centred on the rise axis. An axial low-velocity anomaly at depths of 1–3 km varies in amplitude along the axis, consistent with a zone of higher crustal temperatures midway between two discontinuities in the morphology of the rise axis. This apparent thermal segmentation along axis is consistent with injection of mantle-derived melt midway along a locally linear, 12-km-long segment of the rise.