Each year, Chlamydia trachomatis causes ~3 million new infections and results in more than 1 billion dollars in medical costs in the United States. Repeat or persistent infection occurs in 10%-15% of women who are treated for C. trachomatis infection. However, the role played by antimicrobial resistance in C. trachomatis treatment failures or persistent infection is unclear. With researchers in the field, we reviewed current knowledge and available approaches for evaluating antimicrobial resistance and potential clinical treatment failures for C. trachomatis. We identified key research questions that require further investigation. To date, there have been no reports of clinical C. trachomatis isolates displaying in vitro homotypic resistance to antimicrobials, but in vitro heterotypic resistance in C. trachomatis has been described. Correlation between the results of existing in vitro antimicrobial susceptibility tests and clinical outcome after treatment for C. trachomatis infection is unknown. Animal models may provide insight into chlamydial persistence, since homotypic resistance against tetracycline has been described for Chlamydia suis in pigs. Evaluating C. trachomatis clinical treatment failures, interpreting laboratory findings, and correlating the 2 clearly remain extremely challenging undertakings.