It is known that the texture of cheese changes as a function of pH. Our objective was to determine the differences in the arrangements of protein and fat between a medium pH cheese (Cheddar cheese) and a low pH cheese (feta cheese). Cheese was made using 16-kg aliquots of milk and the make procedure modified to produce cheddar cheeses with a range of pH values as well as making a feta cheese. Samples of curd were collected throughout the cheese making processing, starting from before cutting the curd and during cheese storage. Samples were fixed in glutaraldehyde, then dehydrated, heavy metal stained, embedded and sectioned, and multiple fields observed using transmission electron microscopy. During initial curd formation the characteristic fine stranded network of aggregated casein micelles was observed with fat globules entrapped between the protein strands. As the cheese manufacture continued, and the curd particles contracted and whey was expelled, the initial protein strands apparently coalesced into thicker strands and the casein micelles tended to lose their individual identity. This same general pattern continued throughout manufacture and into the storage period. After 3 mo of aging the cheddar cheeses ranged from pH 4.9 to pH 5.2. There were variations in protein arrangements observed within individual cheese samples as is typical in microstructure of dairy foods. No observable differences in structural arrangements outside this natural variability were apparent between the Cheddar cheese of lowest pH to the highest pH. In contrast, the microstructure arrangements of the proteins in feta cheese were very different to those in Cheddar cheese. In feta cheese, there is a more openness present in the protein network with the appearance of the protein regions having a looser nature; that is, not having large coherent regions of connected protein. This was related to feta cheese having a pH below that at which the caseins are acid precipitated and as they become less soluble in the surrounding serum phase of the cheese. These differences in protein arrangements observed using electron microscopy helps explain the crumbly texture associated with low pH rennet-set cheeses.