BioPAX is a standard for communicating the knowledge about biochemical processes. The BioPAX Validator is to help detect and fix syntax and non-trivial semantic issues introduced in the course of biological pathway data modeling, mapping, and exporting to BioPAX. High quality pathway knowledge is easier to analyze and merge at a much greater level of detail and with more generic, standard tools. The BioPAX Validator contains dozens of custom rules, some of which cannot be expressed in OWL or other rule definition languages. These rules come from BioPAX Level3 specification and the community best practice, are expressed in plain Java and embraced by the validator's original cross-cutting error reporting framework. The rules are, basically, generic Java classes built around Paxtools API. The BioPAX Validator can run online, from command line, or integrated into other java applications as a library. The Validator always converst BioPAX Level1, Level2 to Level3 internally, before it checks Level3 rules; and one can get the Level3 result back along with errors and warnings.