A content-balancing accuracy index, called Q(9), has been proposed to evaluate algorithms of protein secondary structure prediction. Here the content-balancing means that the evaluation is independent of the contents of helix, strand and coil in the protein being predicted. It is shown that Q(9) is much superior to the widely used index Q(3). Therefore, algorithms are more objectively evaluated by Q(9) than Q(3). Based on 396 non-homologous proteins, five algorithms of secondary structure prediction were evaluated and compared by the new index Q(9). Of the five algorithms, PHD turned out to be the unique algorithm with an average Q(9) better than 60%. Based on the new index, it is shown that the performance of the consensus method based on a jury-decision from several algorithms is even worse than that of the best individual method. Rather than Q(3), we believe that Q(9) should be used to evaluate algorithms of protein secondary structure prediction in future studies in order to improve prediction quality.