Capsicum chinense Jacq. and C. baccatum var. pendulum fruits are widely used in the food and processed food industry, in Peru, but their seeds and placentas are discarded as residues. This study aimed to quantify the proportion of edible (pericarp) and non-edible (seeds, placenta and interlocular septa) parts of the fruits, in market condition (semi-dried fruits of C. chinense and fresh fruits of C. baccatum), as well as to quantify the capsaicinoids and their pungency, in extracts of each fruit part previously dried. The pericarp represents 63 % and 85 % of the fruit, respectively for C. chinense and C. baccatum. The placenta stands for ~10 % of the fruit in both species, whereas, for the seeds, the index is 23 % in C. chinense and 5 % in C. baccatum. The content of capsaicinoids and pungency vary among the fruit parts and the species. High contents of capsaicinoids and pungency are found in non-edible parts of the fruit, mainly in the placenta (79 % in C. chinense and 51 % in C. baccatum). Regardless of the fruit part and species, the capsaicin was the major component of capsaicinoids (4,399 ug g−1 and 1,582 ug g−1 of the dry weight in C. chinense and C. baccatum, respectively), while dihydrocapsaicin and nordihydrocapsaicin reached a lower content. C. chinense contains more capsaicinoids and, thus, a much higher level of pungency than the C. baccatum fruits.