Online databases have been increasingly used as a key resource in the search for health information. The current study aims to compare the use patterns of online databases between physicians and nurses. A structured questionnaire was mailed to physicians and nurses of randomly selected regional hospitals in Taiwan. Valid questionnaires with complete answers were collected from 544 physicians and 1,573 nurses from November 2008 to February 2009. In general, physicians made more use of online databases than nurses (p < 0.001). They more often accessed English-language online databases (p < 0.001), including MEDLINE, MD Consult, UpToDate, Cochrane Library and ProQuest. On the other hand, nurses accessed Chinese-language online databases more frequently than physicians (p < 0.001). Using a multivariate logistic regression model to adjust the personal characteristics, we found that nurses more often accessed Chinese-language online databases than physicians. Physicians used online databases to locate health information the most for clinical practice (76.6%), followed by instruction preparation (63.3%), and research (57.0%). Nevertheless, nurses used such databases more often for class assignments (66.4%) and clinical practice (55.8%). In conclusion, the behavior and motivation of access to online databases varied between physicians and nurses. Our findings provide evidence in the strategies to enhance the accessing of online databases.