The incidence of immune disorders is growing parallel with practices associated with westernization, such as dietary changes, increased use of antibiotics, or elevated rates of Cesarean section. These practices can significantly impact the gut microbiota, the collection of bacteria residing in the human gastrointestinal tract, and subsequently disrupt the delicate balance existing between commensal flora and host immune responses. Restoring this balance by modifying the microbiota has thus emerged as a promising therapeutic approach. Here, we discuss the interaction between gut commensals and immunity, along with the potential of different interventions on the microbiota as treatment for inflammatory and allergic diseases.