What's a rare gram negative rods mean? it was taken vaginally via gram stain.

This could be normal: Bacteria are classified, broadly, as being gram-negative or gram-positive (retains violet dye color after staining--gram stain-- a lab slide with specimen on it). And either being rod (cylindrical/barrel shaped) or spherical (cocci) when viewed under a microscope. Gram negative rods are very common in the genital tract, and it sounds like you don't have too many. I say probably normal. Good wishes