Pipeline Pilot is the industry leading enterprise platform for the automation of scientific workflows. It is designed to be open and extensible and following a fruitful joint development program between SciTegic and ChemAxon, a suite of components are now available that allow the power of the ChemAxon tools to be used within the data pipelining environment. In particular we have taken advantage of the sophisticated chemical representation of both products, and their Java APIs to produce a tight integration. In this talk we will demonstrate a number of components and discuss their implementation details, ChemAxon property calculators and structure manipulators are integrated using the Java APIs to send each molecule to the calculators and to set the return property values on the Pipeline Pilot data record. Components include property calculations, molecular ionization, molecular standardization and microspecies calculation, JChem Base integration uses the Java API to automate searching and data upload. JChem Cartridge. ODBC integration components use Pipeline Pilot to generate the SQL needed to automate search and upload functions. MarvinSketch. Pipeline Pilot Webport, an interactive web client for end user access to protocols, takes advantage of Marvin to allow chemists to input queries graphically for upload and processing within protocols. Integration with Pipeline Pilot allows for the automation of tasks that use the ChemAxon technology. Sophisticated applications can be built by using the ChemAxon technology together with SciTegic’s cheminformatics, bioinformatics, text analysis and reporting capabilities and all the capabilities of SciTegic’s 20+ other software partners in a single workflow.