This chapter discusses biases that are of particular importance in the field of pharmacology, the most important of which is confounding by indication. How can researchers delineate those side effects owed to a drug from effects of the disease the drug is treating? A related bias occurs when early symptoms of disease are being treated by a drug that is later falsely implicated as causing the disease (protopathic bias). The adverse event reporting system (AERS) is often used to detect drug effects and one bias, the Weber effect, is reviewed.