This is from a long time friend (Chief of Homicide) (Chief of Police) (Certified by FBI as a polygrapher) whom I trust 100% and believe 100%.
It doesn't matter if you are taking drugs or not. First, the polygrapher establishes a baseline - even if you take Zanax, they can still establish a baseline of you, on Xanax. The tests are read from your baseline, not some statistical national average.
Does that make sense? Did I explain it correctly?
When you ask Bob if his name is Earl, when he answers "no", he establishes a baseline. When he is asked if his name is "Bob" and he answers "yes" he establishes another. A serious of questions that the polygrapher already knows the answer to, are asked and answered to establish the responses on the graph. Even if you are taking Xanax, when you lie, the graph moves.
I'll try to think of an analogy to explain what I am saying. It doesn't makes sense when I read it myself.