The purpose of the current study was to demonstrate the antiproliferative and apoptotic effects of gentiopicroside in OVCAR-3 human ovary cancer cells. The effects on mitochondrial membrane potential loss and expression levels of various apoptosis-related proteins were also studied. The antiproliferative effect of gentiopicroside in OVCAR-3 cells was evaluated by MTT cell viability assay. Phase contrast and fluorescence microscopy techniques were employed to study the effect of the compound on cellular morphology and apoptosis. Flow cytometry using rhodamine-123 dye was used to measure changes in mitochondrial membrane potential (Δψm). Western blot analysis detected the changes in the expression levels of various proteins. The results indicated that gentiopicroside induces potent cytotoxic effects in OVACR-3 cells in a time-as well as dose-dependent manner. Fluorescence microscopy using acridine orange and propidium iodide double staining revealed that gentiopicroside induces moderate and extensive apoptosis in OVCAR-3 cells at lower and higher concentrations respectively. Gentiopicroside also induced potent depolarizing effects on the mitochondrial transmembrane potential with the percentage of depolarized mitochondria increasing from 5.2% in untreated cells to 16.7%, 44.5% and 67.3% in cells treated with 20, 40 and 100 μM dose of gentiopicroside respectively. Gentiopicroside treatment led to up-regulation of cleaved PARP-1, cytochrome c, caspase-3 and caspase-9 and down-regulation of NF-kB and Bcl-2 in a dose dependent manner. The current results indicate that gentiopicroside exerts potent anticancer and apoptotic effects in OVCAR-3 ovary cancer cells via disruption of mitochondrial membrane potential and altering the expression levels of several apoptosis-related proteins.