Raw, pre-roasted and roasted Cocoa samples were separated into four different molecular weight fractions (> 30, 30-10, 10-5 and < 5 kDa) with ultrafiltration and tested for their antibacterial, mutagenic, as well as their radical-scavenging effects. Radical-scavenging effects were tested with electro paramagnetic resonance spectroscopy, anti-mutagenicity in the Salmonella microsome assay (with and without metabolic activation), and antibacterial effects by incubating the fractions with several strains of Bifidobacteria, Enterobacter and Escherichia, and observing their growth. The radical-scavenging activity and reducing substance concentrations increased, particularly in the 5-10-kDa roasted fraction. Chromaticity testing elucidated that the 10-5-kDa fraction was one of the darkest fractions. The Salmonella microsome assay showed neither mutagenic nor anti-mutagenic effects in any of the samples at any of the different concentrations applied when using TA98, TA100 and TA102. All fractions reduced the growth of pathogenic bacteria, in particular at the highest concentration of 100 microg/mL; however, the same trends were also observed for Bifidobacteria.