Fourier domain techniques have increasingly gained attention in the optical coherence tomography field. This is mainly due to demonstrated sensitivities of two to three orders of magnitude greater than conventional time domain techniques. FDOCT images are plagued with two sources of ambiguity and artifact. First, complex conjugate ambiguity arises from the Fourier transform of the real-valued interferometric signal. This ambiguity causes a superposition of reflectors at positive and negative pathlength differences between the sample and reference reflectors. Secondly, the source spectral shape and sample autocorrelation terms appear at DC, there by obscuring reflectors at zero pathlength difference. In this paper, we show that heterodyne detection in swept-source OCT (SSOCT) allows for the resolution of complex conjugate ambiguity and the removal of spectral and autocorrelation artifacts. We show that frequency shifting of the reference arm optical field, by use of acousto-optic modulators, upshifts the cross-interferometric signal to a user-tunable electronic frequency that corresponds to a adjustable electronic pathlength mismatch between the interferometer arms. This electronic pathlength mismatching recenters the A-scan at an offset that can be far from DC, which effectively resolves the complex conjugate ambiguity problem. Additionally, spectral and autocorrelation terms still reside near DC, which allows them to be removed by high-pass filtering. We also show that complex conjugate ambiguity resolution via frequency shifting is immune to falloff induced by finite source linewidth in SSOCT.