The aim of this work was to explore the variations in milk FA concentration according to the rate of pasture utilisation and the cows grazing selection. Two equivalent groups of nine dairy cows were assigned to a long duration (LD) of paddock utilisation (17 days) on heterogeneous pasture, common on extensive rotational grazing systems, or to a medium duration (MD) of paddock utilisation (7-10 days) on a more intensively managed pasture, usual on intensive rotational grazing systems. Grazing selection was characterized at the beginning and at the end of each MD paddock utilisation and at the same dates for LD. Individual milk samples were collected the first three days and the last two days of grazing on each MD paddock for both systems. A principal component analysis (PCA) was performed on milk fatty acid (FA) concentrations and grazing selection data, aiming to highlight their relationships. The LD samples were poorly separated by the PCA according to the day of paddock utilisation, because of small variations in LD milk FA composition. The free-grazing selection allowed the LD cows to ingest herbage with a quite constant nutritional value throughout the experiment. In contrast, the PCA showed a marked separation between samples from the beginning and from the end of each MD paddock utilisation. The MD cows grazed “by layers” inducing a rapid decrease in the nutritive quality of ingested patches during paddock utilisation, with consequently important variations in milk FA composition. Furthermore, an abrupt change in milk FA composition was observed in MD milk when cows were moved to a new paddock. The more stable milk FA concentrations across the LD paddock utilisation could be more favourable for farmhouse cheese making management.