The uniqueness of ruminant milk lipids is based on their high concentration of CLA. Maximal CLA concentrations in milk lipids require optimal conditions of ruminal fermentation and substrate availability, conditions like those present in pasture-fed cows. Our previous work showed that farm management (indoor feeding vs. pasture feeding) markedly influenced the CLA concentration. In this study, the objective was to evaluate the influence of the farm management system as dependent on different locations. Milk samples from different locations (Thuringia and the Alps, representing diverse altitudes) were collected during the summer months and analyzed for FA profile and CLA isomer distribution. The proportion of PUFA and total CLA in milk fat was significantly lower in milk from indoor cows compared with the pasture cows in the Alps. The trans-11 18:1 in milk fat of Alpine cows was elevated, in contrast to lower values for trans-10 18:1. Milk from cows grazing pasture in the Alps was higher in EPA and lower in arachidonic acid than milk from indoor-fed cows. The proportion of cis,trans/trans,cis isomers of CLA was 10 times higher from the indoor cows than from the Alpine cows. In addition to the major isomer cis-9,trans-11, this difference also occurred for the trans-11,cis-13 isomer, which represented more than a fourth of the total CLA present in milk fat. This is the first report showing a special isomer distribution in the milk fat of cows living under very natural conditions. We hypothesize that the CLA isomer trans-11,cis-13 is formed in large quantity as a result of grazing mountain pasture, which is rich in alpha-linolenic acid.