This paper conceives national systems of higher education as stratified populations of organizations. This stratification is a structural component of ‘horizontal inequality’ in higher education, and may be exacerbated by current pressures for colleges and universities to compete for resources and status. To explore this structural inequality, we compare the level of stratification in financial resources across four-year institutions in Canada and the United States over a 35-year period (1971–2006). Our analyses provide a first-look at this form of stratification, employing Gini coefficients, Lorenz curves, and boxplots. Our results provide new and compelling evidence of increasing structural stratification, even in Canada's predominantly publicly funded postsecondary system. Findings indicate that the distribution of resources is far more stratified in the American system, and that both systems have become more stratified over time. We conclude by situating structural inequality within more general processes of stratification in education.