Background: Liquid aspiration during swallowing has been linked to pneumonia, the most common cause of infectious death in the elderly. This paper examines the key issues in the design and implementation of the first multisite, randomized behavioral trial in dysphagia in an aging population. The study evaluated two commonly used treatments with respect to short-term and long-term management of liquid aspiration and subsequent pneumonia in dysphagic geriatric participants with dementia and/or Parkinson's disease. Methods: Discussed are lessons learned during the conduct of this trial and include (1) ethical and methodological design issues, (2) pragmatic implementation of procedures and forms, (3) importance of multiple communication and monitoring strategies, (4) response to funding issues, and (5) changes in staff and facilities. Results: In order to complete this trial the researchers were required to provide more support than anticipated in tasks such as completion of regulatory requirements by sites, supplementing site staff to identify potential study participants using a 'circuit rider' approach, continued recruitment of new sites and staff throughout the course of the trial, adapting forms and procedures and managing within economic constraints in a changing trial environment. Limitations: Many of the challenges faced by the researchers were not anticipated when the study began. Successful strategies are described for these unanticipated difficulties, based on retrospective evaluation. Conclusions: Successful conduct of clinical trials in long-term care environments that are heavily impacted by changes extraneous to the trial design and with staff typically new to clinical trials is possible but success depends on logistical flexibility.