Optical coherence tomography (OCT) provides micrometer-scale structural imaging by coherent detection of backscattered light. Molecular contrast in OCT has been demonstrated using transient absorption, coherent anti-Stokes Raman scattering, and second-harmonic (SH) generation. The sensitivity of molecular contrast signals can be enhanced by use of Fourier domain techniques. We have constructed a spectrometer-based Fourier domain SH-OCT system for simultaneous acquisition of the fundamental and SH signals. We report a >30 dB increase in SH sensitivity over a similar time domain SH-OCT system and demonstrate contrast between cartilage and bone using collagen as the contrast agent.