Milk protein is very important to the dairy industry. Milk protein synthesis is impacted by animal genetics, but is less responsive to nutrition. In a previous study using thiazolinedione (TZD) trying to overcome the milk fat depression effect of trans-10,cis-12 CLA we observed an increase in milk protein content in lactating ewes treated with TZD. This study used a specific chemical PPARγ agonist and CLA to evaluate their effect on expression of milk protein genes (caseins and whey) and their interaction. Twenty-four crossbred lactating ewes (60 ± 0.45 kg body weight) 70 ± 3 DIM, producing 1.2 ± 0.34 kg of milk/d were randomly assigned to one of the 4 treatments (n = 6/treatment) for 7 d. Treatments were: 1) Control (intravenous infusion of 100 mL/d of saline); 2) TZD (Rosiglitazone, intravenous infusion of 4 mg/kg of BW per d in 100 mL of saline); 3) CLA (27 g/d orally dosed methyl ester containing 29.9% of trans-10,cis-12 CLA and 29.8% of cis-9,trans-11); and 4) TZD+CLA. Mammary biopsies were taken, RNA was extracted, cDNA synthesized and qRT-PCR analysis conducted for casein genes (CSN1S1, CNS1S2, CNS2, CNS3) and whey proteins genes [β-lactoglobulin (BLACTO) and α-lactalbumin (LALBA)]. Compared with control, TZD increased milk protein concentration 18.7% and expression of CSN1S1 (P = 0.05), CSN1S2 (P = 0.01), CSN2 (P = 0.01), CSN3 (P = 0.03) and BLACTO (P = 0.02) by 4, 8.6, 5, 4.9 and 4.7 fold, respectively. CLA increased the expression of CSN1S2 (P = 0.03), CSN2 (P = 0.001), CSN3 (P = 0.01) compared with control in 5.5, 5.3 and 3.9 fold, respectively. TZD+CLA tended (P = 0.06) to increase milk protein concentration 11.5% compared with control, but decreased expression (P = 0.05) of all genes studied. Overall, TZD positively affected mammary expression of genes encoding the major milk proteins, while CLA had a partial effect