The similarity of a pair increases with its commonalities and decreases with its differences (Tversky, 1977; Psychological Review). This research addressess how the commonalities and differences of a pair are determined. We propose that comparisons are carried out by an alignment of conceptual structures. This view suggests that beyond the commonality-difference distinction, there is a futher distinction between differences related to the common structure (alignable differences) and differences unrelated to the common structure (nonalignable differences). In two experiments, subjects were asked to list commonalities and differences of word pairs and/or to rate the similarity of these pairs. Three predictions for this task follow from the structural alignement view: (1) pairs with many commonalities should also have many alignable differences, (2) commonalities and alignalbe differences should tend to be conceptually related, and (3) alignable differences should outnumber nonalignable differences. The data support the structural alignment proposal. The implications of these findings for theories of similarity and of cognitive processes that involve similarity are discussed.