The objective was to determine the differences in fatty acid (FA) profiles in subcutaneous adipose tissue (AT) between pregnant women with polycystic ovary syndrome (PCOS) and those without PCOS. FA profiles of AT samples from 13 PCOS and 32 non-PCOS, all of whom underwent caesarean section were compared using gas chromatography. Age and BMI in the two groups were similar. Twenty-one FAs were detected and the total saturated FA percentage of experimental groups was similar. While the total monounsaturated FA (MUFA) (p < 0.0004) and desaturase index (18:1 cis-9/18:0; p < 0.03) were higher in PCOS women than non-PCOS women, total polyunsaturated FA (PUFA) was lower in PCOS than non-PCOS women (p < 0.004). Docosahexaenoic acid level of the two groups was similar while α-linolenic acid and eicosapentaenoic acid levels were significantly (p < 0.05) lower in PCOS. Total trans-FA, C18:1 t9 and C18:2t were lower in PCOS women (p < 0.05). These results indicate differences in desaturase index, MUFA and PUFA, especially n-3 FA in AT between age and BMI-matched pregnant PCOS and non-PCOS pregnant subjects. Further studies are warranted to replicate these findings and to investigate potential changes in these profiles in non-pregnant PCOS women.