Crohn's disease and ulcerative colitis, the two most common inflammatory bowel diseases (IBD), are characterized by chronic relapsing inflammation. Although recent progress regarding the therapeutic approach to these diseases has been made in the development of biologic therapies, not every patient responds well, resulting in a high percentage of ineffectiveness. Even though the immunological cascades range between the current pharmacological agents for IBD treatment and the constant research for more possible pharmacological targets, a lot of progress still needs to be made regarding the correct therapeutical choice for each individual patient. Therefore, it is still important to find proper, inexpensive, and measurable biomarkers, in order to be able to assess the efficacy of these therapies, to make personalized choices, as well as to avoid potential adverse drug reactions and side effects. The biomarkers that are available in the present vary; metabolic, microbial, cytokine-related, genetic, disease-specific and drug-specific. This review presents the existing biological agents for IBD and focuses both on the cascades affected by each biologic agent and on the different markers that have been found to be indicative of their effectiveness.