The published ice core records for Quelccaya, Peru are shown to contain numerous errors in annual layer determination, introduced by the subjective methodology of the original analysis. A new methodology is presented that aligns and then merges d18O sample measurement profiles from the two Quelccaya cores. Absolute dating of the stratigraphy is established by comparison of prominent dust anomalies with documented earthquake reference-marker events. The results demonstrate that the original sample measurements can register a comprehensive millennial climate history at sub-annual resolution, thus also offering great potential for clearer interpretations of ENSO signals in tropical Andean ice cores.