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Natural occurrence of yellow mosaic disease was observed on bitter gourd (Momordica charantia). Association of geminivirus with the disease was investigated through polymerase chain reaction using geminivirus-specific primers and Southern hybridization with a probe prepared from the cloned DNA of a known geminivirus. The fruits, leaves and stem of infected and healthy plants were studied for phytochemical composition. The amounts of protein were 49%, 50% and 66% higher, total carotenoids were 36%, 33% and 40% lower, vitamin C were 23%, 48% and 50% lower, total phenols were 28%, 31% and 43% lower, and antioxidant activity were 36%, 48% and 43% lower in the severely virus infected fruits, leaves and stem, respectively, as compared with healthy plants. The loss in the quantity of these phytochemicals was also observed even in mild infected plants, which further increased with the severity of the symptoms. Similarly, ethanol and 50% ethanol soluble extractive were also 25–43% lower in the fruits, leaves and stem of infected plants as compared with the healthy plants. A 45% and 54% lower caffeic acid, and 78% and 59% lower amounts of ferulic acid in the fruits and stem, respectively, and a 25% loss of gallic acid were noticed in the leaves of the severely infected plants.