Background When using a conventional relational database approach to collect and query data in the context of specific clinical studies, a study with a new data set usually requires the design of a new database and entry forms. OpenSDE (SDE = Structured Data Entry) is intended to provide a flexible and intuitive way to create databases and entry forms for the collection of data in a structured format. This study illustrates the use of OpenSDE as a potential alternative to a conventional approach with respect to data modelling, database creation, data entry, and data extraction. Methods A database and entry forms are created using OpenSDE and MSAccess to support collection of coronary surgery data, based on the Adult Cardiac Surgery Data Set of the Society of Thoracic Surgeons. Data of 52 cases are entered and nine different queries are designed, and executed on both databases. Results Design of the data model and the creation of entry forms were experienced as more intuitive and less labor intensive with OpenSDE. Both resulting databases provided sufficient expressiveness to accommodate the data set. Data entry was more flexible with OpenSDE. Queries produced equal and correct results with comparable effort. Conclusion For prospective studies involving well-defined and straight forward data sets, OpenSDE deserves to be considered as an alternative to the conventional approach.