Plant species which depend on vertebrates for dispersing their seeds in flesh fruits to safe sites for establishment often face the trade-off between attracting seed dispersers and preventing their seeds from over consumption by seed predators. Secondary substances such as glycoalkaloids, emodin, and capsaicinoids in fleshy fruits play an important role for regulating this process. There are diverse secondary substances in vertebrate-dispersed fleshy fruits, but they are often the same as those found in the stems and leaves, and mostly belong to the three major categories: nitrogen-containing compounds (e.g. glycoalkaloids and capsaicinoids), phenolic compounds (e.g. emodins and tannins), and terpenoids (e.g. saponins). The content of some secondary substances such as tannins and emodins is abundant in immature fruits, which deters the potential predators or pre-mature disposal by frugivores; the content decreases with the fruit maturity. Other secondary substances (e.g. apocarotenoids) increase with the maturation, which may promote the consumption by dispersers. Secondary substances in vertebrate-dispersed fleshy fruits may modify the relationship between animals and plants by altering the fruit consumability: depending on the type of the secondary substances, the fleshy fruits could be toxic to all vertebrates (non-specific or general toxic) or only to some species (specific or directed toxic). Secondary compounds might be able to regulate animal feeding frequency and the amount of consumption by causing frugivores to leave the fruit plant sooner in a foraging bout; early departure from the plant might reduce the number of fruits consumed by a particular animal, but may increase the overall the likelihood of seed dispersal away from parent plant by other dispersers. Secondary substances in ripe fruit pulp can inhibit pre-dispersal seed germination or enhance post-dispersal seed germination. Gut retention time of seeds in vertebrates could be altered by some secondary substances, permitting either more rapid passage via laxative effects or slower passage rates by constipating effects. The colors, odors, and flavors of the fleshy fruits can be modified by secondary substances, which can attract dispersers by providing foraging and rewarding cues recognized by frugivores. A single secondary substance can have multiple ecological functions. Our knowledge of secondary substances in flesh fruits and their interactions with vertebrate animals are still limited. Future research need to consider diverse aspects of plant secondary substances such as the comprehensive regulatory mechanisms of fruit physiological biochemistry and morphology characteristics to the frugivores; the regulatory mechanisms of secondary substances for plant population and community structure and distribution patterns post dispersal; and the coevolution between the production of secondary substances and their defense and attraction strategies of plants and the selection and consumption of fleshy fruits by vertebrate animals. The research of secondary substances in vertebrate-dispersed fleshy fruits will enhance our knowledge of seed dispersal mechanisms, plant generation and recruitment patterns, and animal-plant interaction and their coevolution.