The principal aim of this work was to compare Caciotta cheeses obtained from cow milk previously subjected to high pressure homogenisation (HPH) at 100 MPa with those produced from raw (R) or heat-treated (P) cow milk. HPH had both direct and indirect effects on cheese characteristics and their evolution during ripening. In particular, HPH treatment of milk induced a significant increase of the cheese yield; moreover, it affected the microbial ecology of both curd and cheese. Compared with the thermal treatment, the HPH treatment resulted in a decrease of about one log cfu/g of yeast and lactobacilli cell loads of the curd. The initial milk treatment also affected the evolution over time and the levels attained at the end of ripening of all the microbial groups studied. In fact, lactobacilli, microstaphylococci and yeast cell loads remained at lower levels in the cheeses obtained from HPH milk with respect to the other cheese types over the whole ripening period. Moreover, HPH of milk induced marked and extensive lipolysis. Cheeses from HPH milk showed the presence of high amounts of free fatty acids immediately after brining. The electrophoretic patterns of the different cheese types showed that Caciotta made from HPH-treated milk was characterized by a more extensive and faster proteolysis as well as a significant modification of its volatile molecule profile. The results obtained and the sensory analysis indicated that HPH treatment of milk was able to differentiate Caciotta cheese or to modify its ripening patterns.