I am currently using an HPLC system to introduce radoiactively tagged analytes to a Flow Scintillation Analyzer. The question I have is, Is anyone aware of a procedure on how to decontaminate my HPLC from Radioactive contamination, other than replacing everything from the autosampler down?

This in part depends on the isotope(s) and column, etc.. you are using.

A practical approach would be to thouroughly clean the apparatus and especially the column as one always does. Remaining activity, in our experience, is so low and also removed so slowly, if at all, that one can ignore it (not necessarily if you get rid of a contaminated column!). If the isotope has a short halflife you may just wait it out.
Regarding detectors: we only have experience with solid scintillator and gamma detectors. The latter is just a teflon tube which is cleaned like the rest of the apparatus. The scintillator can be difficult to clean, but manufacturers have considerable knowlege on that (usually a HNO3 solution).
When you work with radioactivity you will sooner or later learn that trace amounts of chemicals will stick practically irreversibly to just about anything, certainly also to silicas, especially low grade versions.

Thanks for the feed back, I am really not concerned about the column aspect of the system, more with the capillaries in the autosampler and the flow cell. My task is to decontaminate and decommision the HPLC system to be then used in a standard analytical setting. I spoke with the FSA manufacture(Packard). The rep sugested I flush the system with Non Polar Solvents such as HEXANE, MECL2, CHLOROFORM, DMSO,ETC.. I am interested in any known procedures or information dealing with this issue. Thanks to all for your quick responses..mike