The aim of this study was to determine the effect of the housing system and somatic cell count (SCC) on the composition and fatty acid profile of milk. A total of 419 milk samples were collected from one herd of 210 cows; 90 cows were kept in the tie-stall system, and 120 cows were kept in the free-stall system. The cows received the same fodder. Samples were collected four times, in winter. Udder health was evaluated based on SCC. The tie-stall system, mainly due to individual care, was superior to the free-stall system. Milk from cows kept in the tie-stall system had lower (p < 0.01) SCC by 72 ths mL−1 cells than milk from cows kept in the free-stall system. An increase in SCC was accompanied by decreases in daily milk yield and lactose concentration. Milk from cows housed in the tie-stall barn had higher polyunsaturated fatty acid (PUFA) contents and a lower n-6/n-3 PUFA ratio. Milk with a higher SCC contained more PUFAs and fewer monounsaturated fatty acids (MUFAs). Tie-stall housing contributed to an increase in the proportions of acids beneficial to the health of consumers. A comparison of two housing systems for cows on one farm showed that the free-stall system was associated with a higher SCC and a less favorable milk composition and fatty acid profile.
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