Extinction, absorption, and forward and perpendicular light scatter of the blue-green alga Microcystis aeruginosa with different amounts of intracellular gas vacuoles were determined. The amount of gas vacuoles in the cells was controlled by application of pressure. The presence of the gas vacuoles caused a tenfold increase in perpendicular light scatter, and a fivefold decrease in forward light scatter as measured by flow cytometry. Chlorophyll fluorescence showed a 16% decrease. The presence of gas vacuoles did not affect the size of the algae. The absorption spectrum of Microcystis aeruginosa was slightly raised but practically not distorted by the gas vacuoles. The attenuation spectrum, a measure for light extinction by the algal cells, was significantly distorted. The increase of perpendicular light scatter intensity of the cells is a direct consequence of the relatively high scatter of each vacuole, whereas the forward light scatter decrease is attributed to a lower phase-shift factor s̀ of the whole cells, caused by the intact gas vacuoles.