We report the first fully operational system for managing complex chemical content entirely in interoperating XML-based markup languages. This involves the application of version 1.0 of chemical markup language (CML 1.0) and the development of mechanisms allowing the display of CML marked up molecules within a standard web browser (Internet Explorer 5). We demonstrate how an extension to include spectra and reactions could be achieved. Integrating these techniques with existing XML compliant languages (e.g. XHTML and SVG) results in electronic documents with the significant advantages of data retrieval and flexibility over existing HTML/plugin solutions. These documents can be optimised for a variety of purposes (e.g. screen display or printing) by single XSL stylesheet transformations. An XML schema has been developed from the CML 1.0 DTD to allow document validation and the use of data links. A working online demonstration of these concepts, termed ChiMeraL, containing a range of online demonstrations, examples and CML resources such as the CML DTD and schema has been associated with this article ia the supplementary material.