Evidence-based practice (EBP) requires practitioners to identify and formulate questions in response to patient encounters, and to seek, select, and appraise applicable clinical research. A standardized workshop format serves as the model for training of medical educators in these skills. We developed an evaluation exercise to assess the ability to identify and solve a problem requiring the use of targeted skills and administered it to 47 North American junior faculty and residents in various specialties at the close of two short workshops in EBP. Prior to the workshop, subjects reported prior training in EBP and completed a previously validated knowledge test. Our post-workshop exercise differed from the baseline measures and required participants to spontaneously identify a suitable question in response to a simulated clinical encounter, followed by a description of a stepwise approach to answering it. They then responded to successively more explicitly prompted queries relevant to their question. We analyzed responses to identify areas of skill deficiency and potential reasons for these deficiencies. Twelve respondents (26%) initially failed to identify a suitable question in response to the clinical scenario. Ability to choose a suitable question correlated with the ability to connect an original question to an appropriate study design. Prior EBP training correlated with the pretest score but not with performance on our exercise. Overall performance correlated with ability to correctly classify their questions as pertaining to therapy, diagnosis, prognosis, or harm. We conclude that faculty and residents completing standard workshops in EBP may still lack the ability to initiate and investigate original clinical inquiries using EBP skills.