Consumption of cocoa and dark chocolate products has been associated with positive health outcomes including reduced onset of cardiovascular disease, inflammation, diabetes, obesity, and platelet disorders. Cocoa polyphenols, putatively responsible for these beneficial activities, are highly impacted by cocoa variety, agronomic effects and processing history. However, the difference in polyphenol concentration and composition between cocoa products originating from different hybrid clones (selected for high yield) or from different fermentation conditions is not fully understood. Detailed polyphenol characterization including determination of total polyphenol and total procyanidin concentrations, and qualitative and quantitative analysis of (mean) degree of polymerization was conducted. Significant differences in total polyphenol and procyanidin concentrations were observed between five genetic clones grown by the USDA-ARS Cocoa Germplasm Repository located in Mayagüez, Puerto Rico. To facilitate cocoa fermentation research in laboratories distant from cocoa harvesting sites, a laboratory-scale cocoa fermentation model system was developed in this study. This model system used dried, unfermented, cocoa beans and simulated pulp medium as the starting material. The model system supported growth of the essential succession of cocoa fermenting microorganisms and generated similar chemical changes to those observed in on-farm cocoa fermentation. Using this model system, the impact of inoculation with proprietary yeast strains Saccharomyces cerevisiae Lev F and Saccharomyces cerevisiae Lev B on cocoa polyphenol concentration and composition was evaluated. Inoculation with both yeast strains resulted in increased fermentation rate and Lev B inoculation resulted in higher total polyphenol and procyandin contents at the end of fermentation. Overall, the present work addressed the influence of cocoa variety selection and fermentation process conditions on the composition and concentration of polyphenols. These findings will contribute to continued efforts to develop cocoa products with optimized bioactivity and maximum disease preventative effects. / PHD / Annual worldwide cocoa production exceeds four million tons and the cocoa market impacts not only cocoa growing regions, but also countries producing cocoa products. Consumption of cocoa and dark chocolate products has been associated with positive health outcomes including reduced onset of cardiovascular disease, inflammation, diabetes, obesity, and platelet disorders. Cocoa polyphenols, compounds increasingly associated with health benefits, are highly impacted by the variety and processing history of cocoa. However, the extent to which cocoa genetic variety and processing conditions impact polyphenol concentration and composition is not fully understood. Polyphenol characterization was conducted for five genetic varieties sourced from the USDA cocoa germplasm repository located in Mayagüez, Puerto Rico and it was found that genetic variance could contribute to differences in polyphenol concentration. The main focus in this thesis was to develop laboratory cocoa fermentation model system to facilitate cocoa research in laboratories distant from the cocoa growing region. This model system used dried, unfermented cocoa beans and simulated pulp medium as the starting material. The model system was effective in that it supported growth of the essential succession of coca fermenting microorganisms and generated similar chemical changes to those observed in on-farm cocoa fermentation. This model system could be further applied to test the impact of fermentation conditions on cocoa bean quality. The potential for using yeast starter cultures to improve control and consistency of cocoa fermentation was evaluated using the model fermentation system. Yeast inoculation improved fermentation rate, and polyphenol concentration in fermented beans was higher when cocoa fermentation was inoculated with the yeast strain Saccharomyces cerevisiae Lev B. Overall, the present work addressed the influence of cocoa variety selection and fermentation process conditions on the composition and concentration of polyphenols. These findings will contribute to continued efforts to develop cocoa products optimized for maximum health benefits.