Toll-like receptors (TLRs) are key players in innate immunity. They are able to sense different microorganisms ranging from protozoa to bacteria, fungi or viruses. Innate immune responses can directly influence adaptive immune responses. Therefore, TLRs are considered as relevant targets for therapeutic applications in immune diseases: such as autoimmune disorders, allergy, sepsis, and cancer. We here review the recent patents based on the modulation of the toll-like receptors to develop anti-infective (prophylactic and/or therapeutic) agents.