One of the most promising advantages of surface-enhanced Raman scattering (SERS) technique for in vivo biosensing is the multiplexing potential, which is under explored due to the limited availability of near-infrared Raman reporters. Here, we report the synthesis of multiplexing capable and biocompatible SERS nanotags using highly sensitive novel NIR Raman reporters. Two new NIR Raman reporter molecules, Cy7LA, Cy7.5LA are developed to partner with recently synthesized CyNAMLA-381 reporter to construct SERS nanotags with multiplexing capability. These nanotags possess excellent SERS signal stability over a period of one month. As a proof of concept for multiplex targeted in vivo detection, we successfully demonstrated the simultaneous sensing of cancer in living mouse using these three bioconjugated nanotags. To the best of our knowledge, this is the first real demonstration of in vivo multiplex targeted detection using SERS nanotags. Further, in vivo kinetic study of these nanotags in tumor revealed their excellent sensitivity, stability and tumor specificity. These probes also show rapid clearance from the liver indicating their possible excretion. This validation renders our SERS nanotags as an ultrasensitive in vivo nanoprobe for the detection and imaging of multiple biomarkers for early diagnosis of diseases. © 2012 Elsevier Ltd. All rights reserved.