The AIDS Clinical Trials Group designed and implemented a prospective, randomized, strategy trial in antiretroviral-experienced, HIV-infected patients, to evaluate the virologic impact of protease inhibitor dose escalation in response to therapeutic drug monitoring (TDM) with an inhibitory quotient, which integrates both drug exposure and viral drug resistance. In the process of developing this clinical trial several unique challenges were identified that required innovative solutions. The major challenge was the need to integrate resistance testing, pharmacokinetic data, medication adherence, toxicity data, clinical assessments, randomization assignment, and protocol-specified clinical management in a way that could be utilized in real-time by the protocol team, communicated promptly to the clinical sites, and transmitted accurately to the study database. In addition, the protocol team had to address the relative lack of commercially available therapeutic drug monitoring laboratories in the US that were experienced in antiretroviral drug assays, and a lack of familiarity with the principles of pharmacokinetic monitoring at participating clinical sites. This manuscript outlines the rationale for the design of this strategy trial, specific barriers to implementation that were identified, and solutions that were developed, with the hope that these experiences will facilitate the design and conduct of future trials of TDM.