The Cieplak model has been met with mixed reviews, and criticisms of both its basic logic and predictive ability have emerged. The stabilizing interaction of donating electron density into the transition state σ* orbital of a forming bond was immediately questioned, as this interaction has been widely invoked to explain exactly the opposite—the destabilization of bonds. Traditionally, forming bonds are stabilized when they donate electron density from their bonding HOMO into a neighboring antibonding LUMO, not by accepting electron density into their LUMO. To this end, David A. Evans said of Cieplaks proposal: "Structures are stabilized by stabilizing their highest energy filled states. This is one of the fundamental assumptions in frontier molecular orbital theory. The Cieplak hypothesis is nonsense." However, Hahn and le Noble refute this point by invoking the principle of microscopic reversibility, where the process of bond formation and cleavage are fundamentally equivalent in an equilibrium, and little value should be placed on the terms ‘bonding’ and ‘antibonding’, σ or σ*. In another criticism of the model, Houk questions Cieplaks fundamental assumption that C-H bonds are better electron-donors than C-C bonds. This point is still contested and represents another major dispute in the field.
To further refute the Cieplak effect, Houk puts forth a system in which Cieplak's model predicts the wrong product distribution trend. In the case of substituted trans-decalones, electron-withdrawing substituents equatorial at C4 should discourage equatorial attack and yield more axial product, since the ring C–C bonds are deactivated for donation into the forming C-Nuc bond. Experimental evidence, however, shows that axial electron-withdrawing C4 substituents are more directing towards axial attack than equatorial substituents. Since axial orbitals are not aligned for hyperconjugation in this system, Houk rationalized this trend by invoking electrostatic arguments, described below.