Momordica charantia, is widely used as a medicinal plant. Studies have revealed that they contain an array of biologically active proteins like momordin which act as anti-tumor, anti-diabetic, and anti-rheumatic. Since momordin is an active compound, we have made a thorough study on the presence of momordin in the leave and fruit extracts of white and green varieties of the plant. Momordin eluted at 3.84-3.85 min under the standardized HPLC condition. It was found that the momordin was present only in the methanolic extracts of fruit and leave samples and not in the water extracts. The leave samples were found to be contained more quantity of momordin (2878.57 µg/mL) when compared with the fruit extract (72.72 µg/mL). It was also observed that green variety of bitter gourd contained more momordin than white varieties.