Allergic and auto-immune inflammatory diseases are a worldwide medical concern. Present therapeutics are effective in disease maintenance, allowing relief of symptoms, but are frequently accompanied by unacceptable side effects when given chronically for long periods. Immunotherapy for allergies is effective at inducing anergy to some allergens clinically, but for others it is either ineffective or has a risk of an adverse response. Similarly glucocorticoids, and nonsteroidal anti-inflammatory drugs, which are widely used to treat inflammatory auto immune diseases, are associated with debilitating side effects. Nanoparticles, derived from a variety of different molecular approaches, provide a means to deliver drugs to target organs and cells, lowering the dose requirement and potentially overcoming problems associated with systemic drug delivery. Novel therapeutics in the form of small molecules, proteins, DNA or small inhibitory RNAs, are advancing at a rapid rate toward the clinic and may suffer similar problems to those of current therapeutics. A large body of evidence using nanoparticles for delivery in both allergy and auto-immune disease models demonstrates improvement in alleviating disease. Delivery of current anti-inflammatory drugs, as well as novel therapeutics via nanoparticles also show improved attenuation of disease. The several chemically distinct nanoparticle structures, combined with the currently used drugs, the new wave of drug targets, and novel gene targeted approaches may provide the opportunity to discover optimal combinations for treating allergic and inflammatory disease.