Objective: Prolonged use of Kampo medicines containing Gardenia fruit can cause mesenteric phlebosclerosis. A cumulative dose exceeding 5,000 g of Gardenia fruit may trigger this condition. However, the Japanese Pharmacopoeia 18th edition only specifies the minimum geniposide content in Gardenia fruits, making it difficult to assess the risk based solely on the cumulative Gardenia fruit dose. Hence, we evaluated mesenteric phlebosclerosis risk concerning cumulative geniposide intake in the current study. Quantitative analyses were conducted on ethical Kampo extract formulations containing Gardenia fruit. Methods: Ethical Kampo extract formulations containing Gardenia fruit were separately extracted using an H2O/methanol (1:1) solution and the resulting extracts underwent filtration. Each filtrate underwent quantitative, high-performance liquid chromatography analysis. Results: Significant variation was observed in the geniposide quantities among various ethical Kampo extract formulations containing identical amounts of Gardenia fruit in each daily dose. Additionally, the extracts of orengedokuto, kamishoyosan, and bofutsushosan obtained from various companies exhibited maximum differences in geniposide quantities ranging from 1.5- to 2.7-fold. Conclusion: This study highlights the challenges in accurately assessing geniposide levels in ethical Kampo extract formulations containing Gardenia fruit solely based on the daily dose of Gardenia fruit. The potential development of mesenteric phlebosclerosis should be considered based on the cumulative intake of geniposide rather than the cumulative dose of Gardenia fruit. Additionally, the study offers recommendations regarding the optimal geniposide quantities in ethical Kampo extract formulations containing Gardenia fruits.