© 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd. Accurate and timely diagnosis of transplant rejection is essential for the long-term survival of solid-organ transplant recipients. Biopsy is the “gold standard” for the diagnosis of rejection, but this approach is a time-consuming, expensive, and invasive process. An efficient, cheap, and noninvasive tool for monitoring of immune rejection is urgently needed. Circulating miRNA and circulating DNA can be easily amplified and quantified by PCR which could be potential biomarkers for monitoring organ survival and/or immune rejection. In this review, we briefly introduce the origins and characteristics of circulating miRNA and circulating DNA. Furthermore, we review their clinical application and potential as noninvasive biomarkers for rejection in organ transplantation. Finally, we sum up their potential as biomarkers, which may help scientists and surgeons choose the proper biomarker for routine assays.