Recent developments in statistical methodology have facilitated international innovation comparisons. These, however, inevitably reflect both the industrial structure of the underlying economies, and the innovativeness of firms within each element of the industrial structure. The authors consider the extent to which structural differences between economies can influence international innovation comparisons. The impact of structural differences is considered both in conceptual and in empirical terms, with the aid of data from the first and second Community Innovation Surveys (CIS 1 and CIS 2). Conceptual analysis suggests a very restricted range of scenarios under which structural adjustment will be effective. Empirical results are more reassuring, however, suggesting that, although structural effects are in some cases quite large, they do not significantly distort international innovation relativities. The comparisons do, however, highlight significant inconsistencies between different innovation indicators and suggest policy priorities.