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The purpose of this paper is to evaluate the functioning of the main Spanish and Portuguese containers ports to observe if they are operating below their production capabilities.

To achieve the above-mentioned objective, one possible method is to calculate the data envelopment analysis (DEA) efficiency, and the scale efficiency (SE) of targets, and in order to consider the variability across different samples, a bootstrap scheme has been applied.

The results showed that the DEA bootstrap-based approach can not only select a suitable unit which accords with a port’s actual input capabilities, but also provides a more accurate result. The bootstrapped results indicate that all ports do not need to develop future investments to expand port infrastructure.

The proposed DEA bootstrap-based approach provides useful implications in the robust measurement of port efficiency considering different samples. The study proves the usefulness of this approach as a decision-making tool in port efficiency.

This study is one of the first studies to apply bootstrap to measure port efficiency under the background of the Spain and Portugal case. In the first stage, two models of DEA have been used to obtain the pure technical, and the technical and SE, and both the input-oriented options: constant return scale and variable return scale. In the second stage, the bootstrap method has been applied in order to determine efficiency rankings of Iberian Peninsula container ports taking into consideration different samples. Confidence interval estimates of efficiency for each port are reported. This paper provides useful insights into the application of a DEA bootstrap-based approach as a modeling tool to aid decision making in measuring port efficiency.