The development of procedures for assessing factors that contribute to pain and disability is crucial for clinical and epidemiologic studies. The present paper describes a system for in vivo, real-time assessment of pain behaviors integrated with a standardized physical examination for low back pain patients. The principles for measuring five categories of pain behavior--guarding, touching/rubbing, words, sounds and facial expressions--and for parsing the physical examination are described. The system was learned by five observers who then applied it during the physical examinations of 176 patients classified as suffering from sub-acute or chronic pain. The system was also applied to 77 patients in a test-retest consistency study. Measures of guarding, words, sounds and facial expression showed adequate psychometric properties. The test-retest consistency of guarding, sounds and facial expression was moderate-to-good, suggesting that these behaviors were consistent over the test-retest interval and promising for future study. The advantages and limitations of the technique are discussed and ways of modifying it to simplify coding and enhance the accuracy and reliability of its application are suggested. Overall, the technique shows promise for clinical and epidemiologic research.