Background: Research on salivary gland tissue is important, both for maintaining good oral health and for understanding the properties and functions of secretory cells with similar developmental mechanisms and functions. However, research on the pathogenesis of salivary gland disease and the development of therapeutic agents is very insufficient, and no studies have yet reported effective approaches to changes that occur according to the concentration of Matrigel, which is used to mimic the interactions between cells and the extracellular matrix, in three-dimensional organoid culture systems.Methods: We aimed to identify the most suitable concentration of Matrigel for analyzing the morphology and differentiation patterns of organoids prepared using salivary submandibular gland-derived cells after inducing differentiation with or without a specific chemical, Y-27632.Results: In both low and high Matrigel concentration conditions, morphological differences were found between the control group and the Y-27632 treatment group, and the budding structure was also significantly higher in the Y-27632 treatment group. However, more distinct patterns of differentiation appeared in the high-concentration condition.Conclusion: The concentration of Matrigel in the 3-dimensional organoid culture system had a significant effect on mimicking the actual in vivo environment.