The choice of a suitable automated system for a diagnostic laboratory depends on various factors. Comparative workflow studies provide quantifiable and objective metrics to determine hands-on time during specimen handling and processing, reagent preparation, return visits and maintenance, and test turnaround time and throughput. Using objective time study techniques, workflow characteristics for processing 96 and 192 tests were determined on m2000 RealTime (Abbott Molecular), Viper XTR (Becton Dickinson), cobas 4800 (Roche Molecular Diagnostics), Tigris (Hologic Gen-Probe), and Panther (Hologic Gen-Probe) platforms using second-generation assays for Chlamydia trachomatis and Neisseria gonorrhoeae. A combination of operational and maintenance steps requiring manual labor showed that Panther had the shortest overall hands-on times and Viper XTR the longest. Both Panther and Tigris showed greater efficiency whether 96 or 192 tests were processed. Viper XTR and Panther had the shortest times to results and m2000 RealTime the longest. Sample preparation and loading time was the shortest for Panther and longest for cobas 4800. Mandatory return visits were required only for m2000 RealTime and cobas 4800 when 96 tests were processed, and both required substantially more hands-on time than the other systems due to increased numbers of return visits when 192 tests were processed. These results show that there are substantial differences in the amount of labor required to operate each system. Assay performance, instrumentation, testing capacity, workflow, maintenance, and reagent costs should be considered in choosing a system. A utomated instruments offer standardized processing technology for specimen extraction, specimen amplification, and detection of molecular targets (1). Minimal operator interaction is required, improving workflow, test throughput, and overall efficiency of laboratory operations. With clearance by the U.S. Food and Drug Administration and other regulatory agencies in Europe and elsewhere of several systems, automated molecular testing has become routine in clinical laboratory practice, ensuring diagnostic accuracy and improved result turnaround time (TAT). Studies have been published assessing clinical performances of molecular assays (2-8), and workflow and maintenance characteristics of automated instruments (9-16). In addition to performance and instrumentreagent costs, hands-on time required for testing and maintenance, in-process interaction, and time to results and test capacity are key metrics that should be considered because they can influence efficiency and labor costs. In this respect, workflow studies provide quantifiable and objective data to assist in choosing a system that is best suited for a given laboratory.This study was conducted to determine the relative workflow and maintenance characteristics of five automated instruments commonly used for the diagnosis of sexually transmitted infections. For this purpose, the respective second-generation assays for C. trachomatis and N. gonor...