An ongoing debate in the literature on the efficiency of higher education institutions concerns the indicator for research output for use in empirical analysis. While several studies have chosen to use the number of publications as this indicator, others rely on the amount of research grants. The present study investigates whether both measures lead to a similar assessment of universities. In addition, the number of publications belonging to the 10% and 1% most frequently cited papers in the corresponding subject category and publication year are evaluated. We show that there is a high correlation of efficiency values between the estimations using these indicators. This correlation is slightly higher when the efficiency values result from a data envelopment analysis than when they are determined with a stochastic frontier analysis. The results of this study provide helpful guidelines for researchers evaluating the efficiency of universities and are valueable for decision-makers in science policy.