Fluid goat milk submitted to thermal treatment has interesting nutritional properties and a potential expanding market. The present study was aimed to conduct fatty acids profile characterisation of goat milk placed on market. Forty-nine fluid milk samples were collected: 12 pasteurised, 12 pasteurised at high temperature, 11 ultrahigh temperature (UHT) whole milk and 14 UHT semi-skimmed milk. Milk samples were collected at retail level from 7 different companies and from different production batches. After extraction and methilation, fatty acids (FAs) profile was determined on each sample using a gas chromatograph with flame ionisation detector (GC-FID) with high-polarity capillary column. The concentration (g/100mL) of saturated fatty acids (SFAs), monounsaturated fatty acids (MUFAs), polyunsaturated fatty acids (PUFAs), trans fatty acids (t-FAs), and isomers of conjugated linoleic acid (CLA) was determined. N-6/n-3 ratio, atherogenic index (AI) and thrombogenic index (TI) were also assessed. Fluid goat milk lipid profile was characterised by SFAs (68.4% of total FAs), PUFAs (5.3%), MUFAs (21.3%), tFAs (3.6%) and CLA (0.8%). The most represented fatty acids were: 16:0 (24.5%), 9cis-18:1 (18.2%), 18:0 (9.6%), 14:0 (9.5%), 10:0 (9.3%) and 12:0 (4.5%). Nutritional indices were 2.8-6.8 for n-6/n-3 ratio; 2.3-2.9 for AI; and 2.7-3.2 for TI. Milk produced by small scale plants, with no milk fat standardisation, showed greater differences in fatty acid profile as compared to industrial plants milk. Large scale production is characterised by commingled bulk tank milk of different origins and then is more homogeneous. The whole goat milk supply chain should be controlled to obtain milk with fatty acids of high nutritional value.