The post-genomic era presents many new challenges for the field of bioinformatics. Novel computational approaches are now being developed to handle the large, complex and noisy datasets produced by high throughput technologies. Objective evaluation of these methods is essential (i) to assure high quality, (ii) to identify strong and weak points of the algorithms, (iii) to measure the improvements introduced by new methods and (iv) to enable non-specialists to choose an appropriate tool. Here, we discuss the development of formal benchmarks, designed to represent the current problems encountered in the bioinformatics field. We consider several criteria for building good benchmarks and the advantages to be gained when they are used intelligently. To illustrate these principles, we present a more detailed discussion of benchmarks for multiple alignments of protein sequences. As in many other domains, significant progress has been achieved in the multiple alignment field and the datasets have become progressively more challenging as the existing algorithms have evolved. Finally, we propose directions for future developments that will ensure that the bioinformatics benchmarks correspond to the challenges posed by the high throughput data.