A novel 2-stage gravity separation scheme was developed for fractionation of raw, whole bovine milk into fractions enriched in small (SFG) or large (LFG) fat globules. The volume mean diameter of fat globules in SFG, LFG or control (CTRL) milk was 3·45, 4·68 and 3·58 μm, respectively. The maximum in storage modulus (index of firmness) decreased with increasing fat globule size for rennet-induced gels formed from SFG, LFG or CTRL milks. Miniature (20 g) Cheddar cheeses were manufactured using each of the 3 milks. There were no significant (P>0·05) differences in the pH, moisture and fat in dry matter levels between cheeses made using any of the 3 milks, however, the fat content of the cheese made using SFG milk was ~1% lower than that of cheese made using LFG or CTRL milk in each of the 2 trials. Image analysis of confocal scanning laser micrographs of the cheeses illustrated that the star volume of fat globules in the cheeses decreased significantly (P[les ]0·05) as the size of fat globules in the milks used for cheesemaking was reduced. This indicates that it is possible to manipulate the size distribution of fat globules in Cheddar cheese by adjusting the fat globule size distribution of the milk used for cheesemaking. The concentration of free fatty acids (FFA) increased in all cheeses during ripening. At 120 d of ripening, the concentration of FFA varied significantly (P[les ]0·05 and P[les ]0·001 for trials 1 and 2, respectively) with fat globule size, with cheeses made in trial 2 from LFG, SFG or CTRL milks having total FFA levels of 3391, 2820 and 2612 mg/kg cheese, respectively.