Brassica juncea plants transformed with the Arabidopsis ADS1 gene, which encodes a plant homologue of the mammalian and yeast acyl-CoA Delta9 desaturases and the cyanobateria acyl-lipid Delta9 desaturase, were found to have a statistically significant decrease in the level of saturated fatty acids in seeds. The decrease in the level of saturated fatty acids is largely attributable to decreases in palmitic acid (16:0) and stearic acid (18:0), although arachidic acid (20:0), behenic acid (22:0) and lignoceric acid (24:0) were also decreased in the transgenic seeds compared to the negative control lines. As a result, the level of oleic acid (18:1) was slightly increased in the transgenic seed lines compared to the non-transformed controls. However, a decrease in saturated fatty acid is not always accompanied by the corresponding increase in mono-unsaturated fatty acids. For example, palmitoleic acid (16:1), gondoic acid (20:1) and nervonic acid (24:1) were all found to be decreased in transgenic seeds. The levels of linoleic acid (18:2) and linolenic acid (18:3) were also notably changed in the transgenic lines compared to the controls. The present study provides preliminary experimental data suggesting that the Arabidopsis ADS1 encodes a fatty acid Delta9 desaturase and could be useful in genetic engineering for modifying the level of saturated fatty acids in oilseed crops. However, the effect of ADS1 gene expression on seed oil fatty acid composition is beyond the changes of total saturated and mono-unsaturated fatty acids, which suggests a complex mechanism is involved in the regulation of fatty acid metabolism.