The transition states (TS) for several organic reactions (concerted Diels-Alder, 1,2-H-atom shift in ethyl radical, and H-atom transfers from methane and propene to methyl radical) have been optimized on potential energy surfaces that include the counterpoise (CP) correction for basis set superposition error (BSSE). Various molecular orbit methods were used (Hartree-Fock (HF), second order Moller-Plesset, and density functional theory (DFT)) using basis sets varying in size from 3-21G to 6-311++G**. We show that the CP-optimized TSs obtained using small basis sets resemble those obtained using the larger basis sets both in energies and geometries. The geometry of the concerted Diels-Alder TS for ethylene and butadiene becomes more compact upon CP-correction, whereas the apparent TS for the 1,2-H-atom shift in ethyl radical is shown to be an artifact of BSSE (at least at the HF and DFT levels). The TSs for the radical abstraction reactions are shown to move toward product upon CP-optimization, The choice of fragments for the CP-correction is discussed.