BACKGROUND: Searching the Web for documents using information retrieval systems plays an important part in clinicians' practice of evidence-based medicine. While much research focuses on the design of methods to retrieve documents, there has been little examination of the way different search engine capabilities influence clinician search behaviors. OBJECTIVES: Previous studies have shown that use of task-based search engines allows for faster searches with no loss of decision accuracy compared with resource-based engines. We hypothesized that changes in search behaviors may explain these differences. METHODS: In all, 75 clinicians (44 doctors and 31 clinical nurse consultants) were randomized to use either a resource-based or a task-based version of a clinical information retrieval system to answer questions about 8 clinical scenarios in a controlled setting in a university computer laboratory. Clinicians using the resource-based system could select 1 of 6 resources, such as PubMed; clinicians using the task-based system could select 1 of 6 clinical tasks, such as diagnosis. Clinicians in both systems could reformulate search queries. System logs unobtrusively capturing clinicians' interactions with the systems were coded and analyzed for clinicians' search actions and query reformulation strategies. RESULTS: The most frequent search action of clinicians using the resource-based system was to explore a new resource with the same query, that is, these clinicians exhibited a "breadth-first" search behaviour. Of 1398 search actions, clinicians using the resource-based system conducted 401 (28.7%, 95% confidence interval [CI] 26.37-31.11) in this way. In contrast, the majority of clinicians using the task-based system exhibited a "depth-first" search behavior in which they reformulated query keywords while keeping to the same task profiles. Of 585 search actions conducted by clinicians using the task-based system, 379 (64.8%, 95% CI 60.83-68.55) were conducted in this way. CONCLUSIONS: This study provides evidence that different search engine designs are associated with different user search behaviors.