Engineered gold nanoparticles (AuNPs) have recently drawn an increased interest in disease diagnostics and therapies. However, reports on detailed studies of AuNPs regarding their pharmacodynamics, pharmacokinetics, biodistribution, metabolism and potential toxicity are limited. It is common knowledge that the in vivo behavior and fate of various AuNPs are influenced by their surface and size. However, a comprehensive description and understanding of all variables is crucial for their further development toward potential clinical use. In this article, we describe the pharmacokinetics and biodistribution of mesoporous silica-coated gold nanorods functionalized with polyethylene glycol or bovine serum albumin (AuNR@SiO2-PEG and AuNR@SiO2-BSA, respectively) in tumor-bearing balb/c mice. To gain further insight into the pharmacokinetics, biodistribution and tumor uptake, we also compare the results with BSA functionalized gold nanorods (AuNR-BSA) and gold clusters (AuNC-BSA). The results reveal that AuNR@SiO2-PEG have the longest blood half-life and the maximum percentage content in the tumor at 24 h and 3 days compared to other AuNPs. AuNR@SiO2-PEG, AuNR@SiO2-BSA and AuNR-BSA had primarily accumulated in the liver and spleen without apparent metabolism after 3 days, while the content of AuNC-BSA in the liver, spleen and kidneys showed an obvious decrease, indicating a size-dependent metabolism process. Our results demonstrate how to manipulate the size and surface chemistry of AuNPs to prolong their blood circulation time, improve delivery into target organs and achieve a safer design of nanomedicines.