Here, we examine available glacier mass-balance records between 1993 and 2012 for Andes Cordillera, South America (6.5°N–45.8°S), and the sub-Antarctic islands around the northern tip of the Antarctic Peninsula (62.7°S–63.8°S) to determine their recent mass loss and imbalance with the present climate. The mean annual observed mass-balance Ba changed from − 620 ± 390 (1993–2002) to − 740 ± 240 kg m− 2 yr− 1 (2003–2012) and for this past decade showed a decrease in Ba from south to north. These glaciers had a mean accumulation area ratio of 0.42, which is below the AAR value for glaciers in equilibrium, reflecting mean area and volume imbalances of 23% and 27%, respectively. Glaciers in the northern part of Andes Cordillera are most out of balance with the present climate (33%), while glaciers on the sub-Antarctic islands are only slightly out of balance (4%). We identified a spatiotemporal cycle of Ba that distinguishes glaciers on the sub-Antarctic islands from glaciers in the Andes using an Empirical Orthogonal Function analysis. This analysis also revealed that South America should be divided into three individual glacier regions, and not two regions as earlier stated. Overall, the spatiotemporal cycles identified correlate to the multivariate El Niño Southern Oscillation Index instantaneously (zero-year lag-time) and to the Pacific Decadal Oscillation with an approximately eight-year lag-time.