High quality biological pathway knowledge is easier to analyze and integrate at a greater level of detail and with standard software. The BioPAX Validator applies dozens of custom criteria, some of which cannot be expressed in OWL or rule definition languages, to deal with syntax and semantic errors introduced in the course of pathway data modeling. Rules originate from the BioPAX Level3 specification and the community best practice, are expressed as generic Java classes built around the Paxtools API and Spring framework, report errors or warnings in several categories, and can optionally normalize BioPAX models, always auto-converting BioPAX Level 1, 2 to 3. There are also console and Java library version of this tool.