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In the last few decades there have been remarkable advances in the biological and medical fields. Due to this biological revolution, the old trial and error methods routinely used as a tool to discover new drugs are being put aside, as they no longer fulfill the present pharmacological needs. Therefore, new methodologies for drug discovery that make extensive use of data mining are now emerging. Here we describe how data mining can help in the discovery of new drugs, and we give some examples of methods that are currently used, as well as their associated problems. In particular, we will focus on the problem of pharmacophore identification, in which information from diverse sources is integrated to discover the common characteristics that determine the activity of a drug.