Precise repeat airborne laser surveys were conducted over the major ice caps in the Canadian Arctic Archipelago in the spring of 1995 and 2000 in order to measure elevation changes in the region. Our measurements reveal thinning at lower elevations (below 1600 m) on most of the ice caps and glaciers but either very little change or thickening at higher elevations in the ice cap accumulation zones. Recent increases in precipitation in the area can account for the slight thickening where it was observed but not for the thinning at lower elevations. For the northern ice caps on the Queen Elizabeth Islands, thinning was generally <0.5 m yr-1, which is consistent with what would be expected from the warm temperature anomalies in the region for the 5 year period between surveys, and appears to be a continuation of a trend that began in the mid-1980s. Farther south, however, on the Barnes and Penny ice caps on Baffin Island, this thinning was much more pronounced at over 1 m yr-1 in the lower elevations. Here temperature anomalies were very small, and the thinning at low elevations far exceeds any associated enhanced ablation. The observations on Barnes, and perhaps Penny, are consistent with the idea that the observed thinning is part of a much longer term deglaciation, as has been previously suggested for Barnes ice cap. On the basis of the regional relationships between elevation and elevation change in our data, the 1995--2000 mass balance for the archipelago is estimated to be -25 km3 yr-1 of ice, which corresponds to a sea level increase of 0.064 mm yr-1. This places it among the more significant sources of eustatic sea level rise, though not as substantial as the Greenland ice sheet, Alaskan glaciers, or the Patagonian ice fields.