Abstract: It is generally accepted that plastids play a major role in the synthesis of fatty acids. However, the degree of importance of the chloroplast integrity is not yet well established. In order to determine the effects of alterations in the chloroplast ultrastructure on this process Phaseolus aureus seedlings, species very sensitive to phase-shifts between light and temperature, were grown under control (12/12 h, 32/10°C, light/dark) or inverse (12/12h, 10/32°C, light/dark) conditions. Leaf sections were examined with an electron microscope and the fatty acid contents in the leaves and hypocotyls analyzed using a gas chromatograph. The electron microscopy of chloroplasts showed that unlike normal seedling leaves, there were few thylakoid membranes and no stacking of these membranes into grana occurred in the leaves of inverse seedlings. The levels of fatty acids in the leaves of normal seedlings (e.g., α-linolenic acid, 25 to 70 μg g-1) were always higher than those found in inverse seedling leaves (e.g., α-linolenic acid, 10 to 26 μg g-1). However, in leaves of both normal and inverse seedlings rhythmic fluctuations in the levels of fatty acids with 16 to 18 carbon atoms were observed. Furthermore, the fatty acid contents in hypocotyls of both types of seedlings were almost similar throughout the duration of the experiment. These results suggested that the high network density of thylakoid membranes and their stacking in places into grana are not prerequisites for the synthesis and/or conversion of fatty acids but would rather condition an optimal biogenesis rate and that light/dark cycles might be determinant factors in the induction of rhythmic fluctuations in fatty acid levels in plant leaves.