We characterize the effect of quantum interference on the line shapes and measured line positions in atomic spectra. These effects, which occur when the excited-state splittings are of order of the natural line widths, represent an overlooked but significant systematic effect. We show that excited-state interference gives rise to non-Lorentzian line shapes that depend on excitation polarization, and we present expressions for the corrected line shapes. We present spectra of 6,7Li D lines taken at multiple excitation laser polarizations and show that failure to account for interference changes the inferred line strengths and shifts the line centers by as much as 1 MHz. Using the correct line shape, we determine absolute optical transition frequencies with an uncertainty of ≤25 kHz and provide an improved determination of the difference in mean-square nuclear charge radii between 6Li and 7Li. This analysis should be important for a number of high-resolution spectral measurements that include partially resolvable atomic lines. ©2013 American Physical Society.