Data envelopment analysis (DEA), a cross-sectional study design based on secondary data analysis, was used to evaluate the relative operational efficiency of 16 dental departments in medical centers in Taiwan in 1999. The results indicated that 68.7% of all dental departments in medical centers had poor performance in terms of overall efficiency and scale efficiency. All relatively efficient dental departments were in private medical centers. Half of these dental departments were unable to fully utilize available medical resources. 75.0% of public medical centers did not take full advantage of medical resources at their disposal. In the returns to scale, 56.3% of dental departments in medical centers exhibited increasing returns to scale, due to the insufficient scale influencing overall hospital operational efficiency. Public medical centers accounted for 77.8% of the institutions affected. The scale of dental departments in private medical centers was more appropriate than those in public medical centers. In the sensitivity analysis, the numbers of residents, interns, and published papers were used to assess teaching and research. Greater emphasis on teaching and research in medical centers has a large effect on the relative inefficiency of hospital operation. Dental departments in private medical centers had a higher mean overall efficiency score than those in public medical centers, and the overall efficiency of dental departments in non-university hospitals was greater than those in university hospitals. There was no information to evaluate the long-term efficiency of each dental department in all hospitals. A different combination of input and output variables, using common multipliers for efficiency value measurements in DEA, may help establish different pioneering dental departments in hospitals.