Microscopy and permeability studies were performed to further illustrate the cooling effects on rennet casein gel structure and help interpret the rheological observations in the first part of this paper. Samples of gels cooled from 80 to 5 degreesC at four rates (0.5, 0.1, 0.05, and 0.025 degreesC/min) were studied with a confocal laser scanning microscope. A larger number of smaller floes were generated at slower cooling rates, creating more cross-links within a network and corresponding to a stronger gel. Formation of a larger number of smaller floes was hypothesized to result from a greater degree of doublet formation because the system spent more time within the temperature region where doublet formation is favored when cooled at slower rates. The doublets represent sites available for floe growth, similar to nucleation sites for crystal growth. Microscopy results further substantiated that the cooling effects were different from the aging effects because cooling affected floe size, and aging enabled the addition of idle floes into the casein network. The conclusions for the cooling effects on floe size were further supported by permeability tests. A smaller permeability coefficient resulted from smaller floes obtained with a slower cooling schedule. This study showed the importance of controlling floe numbers to modulate the strength of a gel, and cooling rates provide an approach of modulating functional properties when the chemical composition of a system is fixed.