Background: In the present research, we investigated the effects of the ultra-high dilutions (UHDs) on Oryza sativa L. (rice), physiological and biochemical variations. Methods: In order to study the effect of UHDs (Calendula officinalis in the dilution of 3×103X and Arnica montana in the dilution of 2 ×104 X), 28 experiments were designed and statistically analyzed via the Design Expert 7.0.1 software over the general factorial design methodology. Three qualitative factors were studied including the UHDs/placebo usage (A), sterile/non-sterile experimental condition (B) and the type and timing of the UHDs usage (C). The validated analysis was subjected into more studies on the variations in physiological growth, carbohydrate, protein content, pigment production, and amino acid patterns. Results: To evaluate the effects of UHDs on rice, we formed a desirable response percentage from a number of healthy seedling production, and studied the height percentage of the aerial parts and main roots. The statistical analysis resulted in the prediction model which was more than 97% correlates with experimental results. The results showed that the UHDs increased the pH variations, carbohydrate, protein and pigment levels by ~2.5, ~1.5, ~1.4, and ~1.4 fold, respectively. Also compared to placebo, the amount and proportion of amino acids has significantly varied. . Conclusion: Compared to placebo, the UHDs have statistically validated affected the rice germination and seedling growth. Also, they can affect the stress conditions caused by the sterilization process, seedlings entrance into the light and their transition into hydroponic culture medium. The use of UHDs leads to an increase in the production of chlorophyll, as well as carbohydrate and protein content. Moreover, they cause significant variations in the amino acid profile and the production of amino acids along with the photosynthesis, germination, and metabolism processes.