Results of high resolution x-ray diffraction experiments are presented for single crystals of the spin gap compound BaCuSi2O6 in the temperature range from 16 to 300 K. The data show clear evidence of a transition from the room temperature tetragonal phase into an incommensurately modulated orthorhombic structure below ∼100 K. This lattice modulation is characterized by a resolution limited wave vector qIC =(0,∼0.13,0) and its 2 nd and 3 rd harmonics. The phase transition is first order and exhibits considerable hysteresis. This observation implies that the spin Hamiltonian representing the system is more complex than originally thought.