Changes induced by stepwise substitution of hydrogen for fluorine in neutral and protonated dimethyl ethers are analyzed in the light of the Atoms in Molecules (AIM) theory. AIM atomic and bond properties were computed by using B3LYP/6-31++G(d,p)//B3LYP/6-31G(d,p) wave functions. The effects brought about by fluorine substitution on the atomic and bond propel-ties of the C-O-C chain were analyzed, Fluorine substitution was found to strengthen the C-H bonds. The computed proton affinities were related to the charge and energy of the proton. Reorientation of the CFnH3-n groups upon protonation was explained in terms of the balance between anomeric and steric interactions. This interpretation and lacking of F-H bond paths allow the rejection of the previously proposed hydrogen bonding O-H . . .F linkages in these systems, The fluorine substitution destabilizes C atoms in neutral and protonated forms, whereas the O is stabilized in the neutral molecule and destabilized in the cation.