Antibiotics usually have positive risk-benefit ratios, their adverse effects being generally mild and reversible on treatment cessation. However, severe adverse drug reactions (ADR), associated with significant mortality and morbidity have resulted in the withdrawal of several active antibiotics, including new fluoroquinolones. Adverse reactions to antibiotics are often poorly documented. The purpose of this article is to examine current tools for investigating and preventing antibiotic toxicity and to suggest future lines of investigation. Structure/ADR relationships have been investigated with various antibiotics (beta-lactams, macrolides, quinolones, etc.) in an attempt to reduce the risk of adverse reactions. Some reactions can be linked to the drug's stereochemical composition. In the case of quinolones for instance, particularly ofloxacin and its derivatives, experimental data show that individual enantiomers have different toxicities. Another major factor that influences the risk of ADRs in a given population is metabolic variability, due to genetic differences in the relevant drug-metabolizing enzymes. Idiosyncratic antibiotic toxicity can be caused by a chemically reactive metabolite. Recent advances in molecular biology, and especially in individual genomic characterization (DNA chip technology, etc.), could in future be useful for identifying patients who are at a special risk of ADR. Finally, certain pharmacokinetic parameters (AUC, Cmax, etc.) can be used to predict adverse effects.