Macular pigments are measured by spectrally selective lipofuscin detection. Light from a light source that emits light at a selected range of wavelengths that overlap the absorption band of macular carotenoids is directed onto macular tissue of an eye for which macular pigment levels are to be measured. Emitted light is then collected from the macular tissue. The collected light is filtered so that the collected light includes lipofuscin emission from the macular tissue at an excitation wavelength that lies outside the macular pigment absorption range and outside the excitation range of interfering fluorophores. The collected light is quantified at each of a plurality of locations in the macular tissue and the macular pigment levels in the macular tissue are determined from the differing lipofuscin emission intensities in the macula and peripheral retina.