This study investigated the evolution of trans-9 trans-11 conjugated linoleic acid (CLA) from cis-9 trans-11 CLA during methylation and its avoidance through a rapid base methylation of milk fat. The study examined three conditions shown to result in loss of cis-9 trans-11 CLA during methylation namely: temperature, methylation time, water contamination in old reagents and acidic conditions. Three techniques currently used for the conversion of milk fat into fatty acid methyl esters for analysis of CLA content by gas liquid chromatography and a fourth procedure designed to eliminate acidic conditions and to limit methylation temperature and time were used. The four methods were: (i) acidic methylation (AM); (ii) acidic and basic bimethylation with fresh reagents (FBM); (iii) acidic and basic bimethylation with pre-prepared reagents (PBM) and (iv) basic methylation (BM). Each regime was carried out on six milk samples over two periods and methylated 1 ml freeze-dried milk (n=12 per regime). Total CLA was not different across methylation regimes (0·30 mg/ml). Isomer cis-9 trans-11 was higher (P<0·01) with BM than the other regimes and lowest with AM: 21·2, 17·8, 18·8 and 14·7 mg/100 ml for BM, FBM, PBM and AM, respectively. The inverse relationship was shown for trans-9 trans-11 with higher (P<0·001) amounts with AM than the other regimes and lowest with BM: 0·57, 2·55, 2·36 and 3·69 mg/100 ml for BM, FBM, PBM and AM, respectively. The trans-10 cis-12 isomer was also shown to alter with methylation procedure being higher (P<0·001) with AM than the other regimes: 0·43, 0·47, 0·29 and 1·20 mg/100 ml for BM, FBM, PBM and AM, respectively. Validation with known CLA free fatty acid and triacylglycerol standards confirmed that AM resulted in conversion of cis-9 trans-11 to trans-9 trans-11, and also elevated trans-10 cis-12 whilst BM of triacylglycerol CLA did not isomerise cis-9 trans-11 and was comparable to FBM.