A coincidence has been noticed, in two detailed geophysical surveys in the North Atlantic, between the occurrence of relatively low amplitude sea-floor-spreading magnetic anomalies and sparsely sedimented basement highs. Uniformly covered basement on the same isochron a few tens of kilometres away is associated with relatively high amplitude anomalies. It is proposed that the relatively low magnetic-anomaly amplitudes are associated with basement highs that have persisted for millions of years as chimneys surrounded but not covered by blanketing sediments, through which hydrothermal flow vented to the sea floor. Low-temperature alteration associated with the hydrothermal circulation has substantially reduced the remanent magnetization of the penetrated basalts, thereby leading to reduced anomaly amplitudes. This hypothesis provides an alternative explanation to that of Schouten and Denham for the different along-strike amplitudes of some North Atlantic magnetic anomalies, which they explained in terms of variations in the width of the crustal emplacement zone.