The origin of the regioselectivity of the Baeyer-Villiger reaction of α-Me-, -F-, and -CF(3)-cyclohexanones was investigated theoretically (MPWB1K/6-311++G**-PCM(CH(2)Cl(2))//MPWB1K/6-311G**-Onsager(CH(2)Cl(2))). Investigation of the energy profiles of the rearrangement step revealed the reality of the importance of conventional migratory aptitude based on the stabilization capability of partial positive charge generated during the migration step. We have divided the origin of the regioselectivity into two factors: (1) structural stability (steric repulsion, dipole interaction, etc.) and kinetic reactivity (energy barrier from the intermediate, i.e., cation stabilization capability). For α-CF(3)-cyclohexanone, the migration tendency was mostly dependent on the kinetic reactivity; CF(3) substitution greatly increased the energy barrier. Noteworthy is the orientation of the CF(3) group at the transition state. The CF(3) group possessed the axial orientation overcoming the 1,3-diaxial repulsion, probably because of the strong dipole interaction between the CF(3) group and the leaving acid moiety. Striking results in the case of α-F- and -Me-cyclohexanone were that no difference in the energy barriers by the substituents could be observed. Especially in the case of α-Me substitution, structural stability operates in determining the most stable transition state, which is in contrast to the conventional understanding of the migratory aptitude based on the ability to stabilize partial positive charge.