In this paper we present a system for intraocular distance measurement of the human eye in vivo with high sensitivity. The instrument is based on Fourier domain low coherence interferometry (FD-LCI). State-of- the-art FD-LCI systems are limited to a depth range of only a few mm, because the depth range is determined by the spectral resolution of the spectrometer. To measure larger distances (e.g. human eye length) we implemented two separate reference arms with different arm lengths into the interferometer. Each reference arm length corresponds to a different depth position within the sample (e.g. cornea and retina). Therefore two different depth sections, each with a depth range of a few mm can be imaged simultaneously. With the new system axial distances could be measured with a precision of 8 microm. We demonstrate the performance of the instrument by measuring the axial eye length of 9 patients with cataract and compare our results with those obtained using the IOL Master (Carl Zeiss Meditec Inc.).