Many previous studies proposed equations and models to estimate the heat-input of FSW, but their verifications would be still insufficient. In this study, the heat-input was calorimetrically measured during FSW of aluminum alloys with various welding tools having different shapes, and the effect of tool geometries on heat-input was examined. The measured heat-input increased with increasing shoulder diameter, which was in good agreement with many previous works. Interestingly, the heat-input strongly depended on the probe diameter and length. An attempt to correlate the heat-input with the tool surface area was made, virtually showing that the heat-input linearly increased with increasing “effective surface area” defined as (half of shoulder surface area + probe column surface area + probe tip surface area). This result experimentally suggested that the effect of probe dimension on heat-input was unexpectedly high. Moreover, an empirical equation estimating the heat-input during FSW of aluminum alloys from the welding parameters and the tool geometry was successfully established.