An X-ray backscatter imaging system uses frequency modulated X-rays to determine depth of features within a target. An X-ray source generates X-ray radiation modulated by a frequency-modulated bias current. The X-ray radiation impinges upon and is backscattered from multiple depths within the target. A scintillating material receives the backscattered X-rays and generates corresponding photons. A photodetector, having gain modulated by the frequency modulation signal from the local oscillator, receives the photons from the scintillating material and generates an analog output signal containing phase delay information indicative of the distance travelled by the X-rays backscattered from multiple depths within the target. The analog output signal is sampled by an analog-to-digital converter to create a digital output signal. A computer processor performs a discrete Fourier transform on the digital output signal to provide target depth information based on the phase delay information.