Statistical interferometer technique (SIT) is a highly sensitive optical interferometer developed by us capable of measuring sub-nanometer displacements and when applied to plant growth studies revealed nanometric intrinsic fluctuations (NIF). NIF observed in minimum time scale of several tens of seconds is strongly influenced by the environmental conditions. Our earlier experiments with rice under ozone or heavy metal stress, such as cadmium even for a short duration of one hour decreased NIF. In contrast, having a micronutrient, such as zinc increased NIF. Therefore, presence of NIF is found to be a novel phenomenon characterizing plant condition that could appear only under sub-nanometric measurement. In this study, we report the effects of adding a plant growth hormone called auxin. Roots of rice seedlings were exposed to auxin solutions of different concentrations of 0, 1, and 4 μM for 24 hours. Significant increment was seen in NIF for a concentration of 1 μM while a significant reduction was seen in NIF for 4 μM within an hour after immersion of the roots. Application of an inhibitor to auxin called TIBA also resulted in almost immediate reduction of NIF. Current results suggest for NIF affected by the enodgenous hormones to be related to growth, as the action of a growth-related endogenous hormone auxin is chemically inactivated. Thus, NIF not only could be applied to investigate and speedily assess the effects of environmental agents on plant elongation or shrinkage but also could be implicated as one of the possible mechanisms for the origin of NIF itself.