Genetic improvement of sweet potato [Ipomoea batatas (L.) Lam.] is based on recurrent cycles of phenotypic selection and recombination of parents. Metabolite profiling can be used to differentiate chemotypes to assist selection of parents. Chlorogenic acids (CQAs) and coumarins are natural fungicides and insect repellents present in the storage root periderm which can contribute to reduction of post-harvest losses and insect damage. The objectives of this study were: (i) to develop a rapid and reliable analytical technique for screening breeding lines, (ii) to correlate their CQAs and coumarins contents with periderm colour and biotic stress susceptibility, and (iii) to assess variation among clones. A first experiment measured the variation in scopolin, scopoletin, chlorogenic acid (CGA) and three dicaffeoylquinic acids (3,4-, 4,5-, 3,5-diCQA) in 296 breeding lines periderm. CGA (mean of 0.95 µg/mg FW) and 3,5-diCQA (0.86 µg/mg) contents were significantly higher than scopolin (0.50 µg/mg), scopoletin (0.09 µg/mg), 3,4-diCQA (0.09 µg/mg), and 4,5-diCQA (0.16 µg/mg). CGA was significantly and positively correlated with all compounds but especially with 3,5-diCQA (+¿0.812**). All compounds were in significantly higher content in purple-red periderm breeding lines. A second experiment estimated the range of variation among five clones for 39 selected breeding lines. The results confirmed the first experiment. Furthermore, for all six compounds the coefficient of variation in the second experiment were low indicating that they are genetically controlled. CQAs appear to be more interesting compounds compared to coumarins for selecting breeding lines and chemotype assisted breeding should be a useful tool to reduce post-harvest losses and insect damage.