In this paper the influence of store aerodynamics on aeroelastic instabilities, such as flutter or LCO, of the F-16 aircraft is investigated. It seems that even though a detailed store aerodynamic modeling might not change the nature of the flutter mechanism, i.e. the frequency and the structural modes involved in the flutter, the severity of the mechanism, as evaluated by flutter speeds, can change significantly. This conclusion is particularly relevant to stores that undergo large displacement in the flutter mode and have significant lifting surfaces since they have a significant contribution to the generalized aerodynamic forces. This study should enable the IAF to achieve a major improvement in the flutter prediction capability and therefore reduce the amount of required flutter flight tests.