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Precipitation on the South American Altiplano varies at a range of temporal scales. A long-term secular increase in moisture availability from the early/mid Holocene to the present, driven by increasing summer insolation resulting from precessional changes in the Earth’s orbit, has been documented in earlier studies. However, higher frequency Holocene variability is not yet understood. Here we present high-resolution diatom assemblage data from two small Altiplano lakes, Lago Lagunillas and Lago Umayo, indicating changes in effective moisture in the southern tropical Andes at decadal, centennial and millennial timescales throughout the mid to late Holocene. A strong millennial-scale component, similar in pacing to periods of increased ice-rafted debris flux in the North Atlantic, is observed in both lake records, which suggests that regional precipitation and North Atlantic climate variability are coupled at these scales. The interpretation of the higher frequency variability is hampered by the small number of high-resolution continental and marine records for comparison.