Enhanced biocompatibility of nanosized contrast agent with high radiodensity and specific biodistribution is an important parameter for localized tumor imaging and organ safety. Various nanoparticles, especially gold nanorods (GNRs), have been applied for tumor diagnosis. However, their toxicity, nonspecific biodistribution, and easy aggregation are critical issues in cancer medicine. To avoid these issues, encapsulation of the GNRs in the core of nanoscopic mesoporous silica (MS) under ambient conditions, yielding multifunctional nanomaterials for cancer nanomedicine, is a recent and active development. Interestingly, GNR embedded MS nanohybrid (GNR-MS), though a promising material in nanomedicine, is rarely examined for tumor diagnosis, in vivo toxicity, organ safety, contrast ability, and excretion. Herein, we report a systematic in vivo examination of folic acid functionalized GNR-MS (GNR-MS-FA) for localized 4T1 breast tumor diagnosis, organ safety, and excretion using a one-time dose administration. The nanomaterials show good aqueous dispersibility, biocompatibility, high radiodensity, and tumor specific targeting ability ( in vitro as well as in vivo). The in vivo tumor diagnosis and specific biodistribution of injected nanomaterials clearly demonstrates their potential for the visualization of tumors deep in the body of mice. In addition, all organs including the healthy glomerulus of the kidney are observed to be free of tissue injuries thereby indicating the superior biocompatibility of the nanomaterials.