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This paper aims to investigate if the market structure reforms in the Portuguese health system have improved hospital performance and productivity. A robust non-parametric Malmquist index is applied to measure group performance. The significance of the results achieved is examined using a conditional and non-conditional subsampling bootstrapped-based methodology, enhanced by the likelihood cross validation criterion based on the k-nearest neighbors method. The sample contains information about 216 non-corporatized and 176 corporatized Portuguese hospitals for the period 2002–2009. Five models were applied, based on three study dimensions (internment, emergencies and doctor visits). The results show that although corporatized hospitals presented the highest efficiency consistency, they had also the lowest levels of productivity, while the hospitals under the traditional administrative public management system were the ones with the best average performance. However, several best practices were also found in all groups, being the limited companies were often dominated by both noncorporatized and public enterprise entities. Consistent output ranges where all groups present dominance over the others were also identified. It was possible to conclude that the more autonomy the hospital had from the Ministry of Health, the lower was its productivity.

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