The aim of the study was to evaluate the influence of feeding goats diets with different protein levels (11.4, 13.3 and 16.9%) and a small change of fatty acid contents on the concentrations of trans11C18:1 and conjugated linoleic acid (CLA) isomers in milk. The experimental design was 3 × 3 Latin Square. Each 22-day experimental period consisted of 14 days adaptation to the diets and 8 days for milk samples collection. Separation of methylated CLA isomers was achieved using GLC. Milk production was nearly the same when the low- and medium-protein diets were fed, while the high-protein diet resulted in a tendency to increase milk production. The concentrations of atherogenic (A-SFA), thrombogenic (T-SFA) and total saturated fatty acids (SFA) were similar in milk from goats fed the diets containing low- and medium-protein contents, whereas the diet containing the highest protein content resulted in an increase in the daily production of SFA and A-SFA in milk. The concentration and daily production of cis9trans11CLA, trans10cis12CLA, the sum of CLA isomers and usually trans11C18:1 and the sum of trans,transCLA isomers in milk increased as the dietary protein level increased. The higher dietary protein content resulted in the decrease in the concentration ratio of SFA and unsaturated fatty acids (UFA) (SFA/UFA) and tended to the increase in the capacity Δ9-desaturation.