As the incidence of inflammatory bowel diseases and the number of patients treated with anti-TNF agents keep on increasing so are the phenomena of primary non response (PNR) and secondary loss of response (SLR) to these medications. Traditionally PNR and SLR have been managed empirically—that is, switching medications for PNR and increasing the anti-TNF dose for SNR. More recently an approach based on testing drug levels and antibodies to the drug (therapeutic drug monitoring) has gained increasing popularity in the management of inflammatory bowel diseases. However, while this strategy might offer an insight into the mechanisms leading to PNR/SLR it often falls short of providing a simple, reproducible method to manage these issues in clinical practice. Here, we will review the currently recommended therapeutic strategies when using therapeutic drug monitoring; the evidence for and against such approach and the current standard strategies in Rheumatology (the specialty with the largest and longest experience with anti-TNF agents). We will then discuss the possible reasons of the shortcomings of therapeutic drug monitoring and the rationale and need to move the therapeutic target to the disease burden in inflammatory bowel diseases—along with the supporting preliminary evidence. Finally, we will focus on future crucial studies that need to be done to make approaches to PNR/SLR more rigorous and at the same time user-friendly for the practicing gastroenterologist.