Cytokines play a central role in the pathogenesis of inflammatory bowel diseases. For this reason, the vast majority of biological therapies are aimed to block pro-inflammatory cytokines or their receptors. Although these drugs have modified the course of the disease due to their efficacy, a high rate of non-response or loss of response over time is still an important issue for clinicians. In this perspective, many studies have been conducted in recent years to individuate a reliable biomarker of therapeutic response. In this review, we discuss the role of cytokines involved in the pathogenesis and in the therapy of inflammatory bowel diseases, and their putative use as pharmacological biomarkers of therapy responsiveness.