Pancreatic islet transplantation is a promising beta cell replacement treatment for patients with "brittle" type 1 diabetes (T1D) or intractable chronic pancreatitis to restore or preserve pancreatic endocrine function. Early after transplant, a significant islet mass is lost due to an innate inflammatory response, and further loss of the islet graft occurs over time due to immune response, drug toxicity, or metabolic exhaustion. Thus, clinically feasible techniques are essential to monitor islet graft function and survival to maintain appropriate therapy. Currently, islet graft function is monitored using blood glucose levels, insulin and C-peptide levels, and islet imaging. However, these tests are influenced by physiological changes, including beta cell stimulation. Biomarkers that are independent of metabolic stimuli would be more accurate and reliable in detecting islet damage. Antibodies against islet autoantigens are useful but not reliable markers of islet injury due to their presence during the pretransplant period. Several islet-specific proteins such as Glutamate decarboxylase-65, doublecortin, protein phosphatase 1, regulatory (inhibitor) subunit 1A, ubiquitin C-terminal hydrolase-L1, and the high-mobility group box-1 protein have been proposed as candidates to monitor islet damage, but these biomarkers have short half-lives and unreliable detection. Unmethylated insulin DNA has been studied in T1D patients and has been documented as a highly correlative and selective biomarker for beta cell death. More recently, microRNAs (miRNAs) that are selectively expressed in islets have been shown to provide sensitive and accurate quantification of islet damage. Analysis of plasma samples from autologous and allogeneic islet transplant patients has demonstrated the value of miRNA-375 as a specific biomarker to accurately assess islet damage. Use of selective, sensitive, and measurably reproducible biomarkers of islets will lead to effective monitoring of beta cell replacement therapy and may also lead to development of preventative and interventional treatment strategies to improve outcomes.