During stent development, accurate monitoring of the drug concentration in animal tissues can provide critical information on how the drug is released into the circulation and the surrounding tissues. To establish the relationship between the drug concentration and the distance from the stent to the target tissue, a comprehensive strategy was developed for sample collection, sample homogenization and sample storage as well as sample analysis. This strategy was developed with the analytical chemists and animal surgical specialists working together as a team. The optimized sampling process was designed to yield a representative sample, appropriately located and of an appropriate size. The sampling process was also designed to eliminate the potential for carryover and cross-contamination. During sample processing, the analyte solution was spiked into blank tissues using a sharp needle and a gas-tight syringe to prepare tissue quality control samples. These tissue quality controls were then used to evaluate the stability of the drug in solid tissue and homogenate, the homogenization carryover, the cross-contamination and the recovery of the drug during method validation and to monitor the overall process of drug analysis of the swine tissues. This thorough strategy has been applied to the accurate determination of zotarolimus in swine tissues for regulated toxicology studies. The entire process was controlled, including precise tissue sampling, compound-based tissue homogenization, method validation, and the application of the method to regulated toxicokinetics studies. The results demonstrate that analytical chemistry concepts can be successfully integrated into toxicokinetics studies in order to collect precise samples and obtain meaningful results. The strategy can be applied to similar toxicokinetics studies of locally administrated drugs in tissues.