Caffeoylquinic acid compounds are widespread in plants. They protect plants against predation and infection and may have several beneficial functions in the human diet. The contents of chlorogenic acid and the 3,4-, 3,5-, and 4,5- isomers of dicaffeoylquinic acid (DCQA) in the storage root tissues of 16 sweetpotato [Ipomoea batatas (L.) Lam.] genotypes were determined. Averaged over genotypes, the contents of the four compounds were highest in the cortex, intermediate in the stele, and lowest in the periderm. Among the genotypes, chlorogenic acid contents ranged from 16 to 212 μg·g−1 in periderm, from 826 to 7274 μg·g−1 in cortex, and from 171 to 4326 μg·g−1 in stele. The 3,5-DCQA isomer comprised over 80% of total DCQA. In most genotypes, 3,5-DCQA and chlorogenic acid contents were similar in cortex and stele tissues, but chlorogenic acid was lower than 3,5-DCQA in periderm tissue. Among the 16 genotypes, total DCQA contents ranged from 0 to 1775 μg·g−1 dry weight in periderm, from 883 to 8764 μg·g−1 in cortex, and from 187 to 4768 μg·g−1 in stele. The large differences found in a small germplasm collection suggest that selecting or breeding sweetpotato genotypes with high caffeoylquinic acid content is possible. The four caffeoylquinic acid compounds comprised over 3% of the dry weight of storage roots of the sweetpotato relative, bigroot morningglory [Ipomoea pandurata (L.) G.F.W. Meyer], indicating that it may be a good source for the compounds. The effect of DCQAs isolated from sweetpotato and I. pandurata tissue and caffeic and chlorogenic acid standards were tested in proso millet (Panicum milliaceum L.), Fusarium solani (Sacc.) Mart., and bacterial growth bioassays. Caffeic acid, chlorogenic acid, and 3,5-DCQA were most inhibitory in millet and F. solani bioassays, but 3,5-DCQA was the least inhibitory compound in bacterial growth bioassays. Their activity in the bioassays suggests that the caffeoyl quinic acid compounds contribute to the allelopathic potential and resistance to root diseases of some sweetpotato clones.