New pharmaceutical approaches, such as biotechnology industry, genomic and proteomic studies, require the development of new analytical and preparative tools that should allow the resolution and the characterisation of complex sets of molecule mixtures in a high-throughput mode with the isolation of a single substance from complex matrices in a high degree of purity, low costs and wide availability. In this review we discuss the design of a tailor-made peptide by focusing our attention on the bioinformatic techniques and combinatorial approaches. Then synthesis, purification and characterisation of peptides with recognition properties are discussed by considering different approaches and their fitness to drug design. Moreover, the development of affinity devices and the discussion of their characteristics to optimise the purification phase are reported. Applications of peptide ligands that bind pharmaceutical compounds (i.e. therapeutic proteins, monoclonal antibodies, hormones) are described and analytical tools mentioned and evaluated. Future perspectives, in particular alternative applications of peptide ligands and their substitution with peptidomimetic compounds, are described.