Physicians as well as laypeople use both general purpose and specialised web-based search tools when confronted with medical questions. FindZebra.com is a tool for generating hypotheses about rare disease diagnosis. It uses freely available high quality curated information on rare diseases and open source information retrieval software (Apache Lucene Solr) tailored to the problem. FindZebra is intended primarily for physicians and other professionals concerned with diagnosis of rare diseases. Our benchmarking against several search tools (Google search, PubMed and http://omim.org) shows that FindZebra has higher performance in retrieving the correct diagnosis when queried with symptoms [1, 2]. Our findings indicate that the ranking algorithm used is the most important factor for the success.