A hierarchy differences visualization system and method for visualizing differences between two hierarchical structures based on similarity metrics. The two hierarchical structures are merged into a merged hierarchical structure and differences between the two hierarchical structures are computed and displayed in a user interface using node visualization metrics. In addition, at least one path is computed to a root of the merged hierarchical structure from a selected node and displayed in the user interface. The user interface uses various node visualization metrics including color, shapes, size, underlining, strikethrough, and text transparency. In some embodiments the hierarchical structures are tree structures and the similarity metric is structural uncertainty including location uncertainty and sub-tree structure uncertainty. The location uncertainty of a node is indicated by a color of the node label and sub-tree structure uncertainty of a node is shown by various levels of transparency of node labels.