Wavelength scanning interferometry offers many advantages over traditional phase shifting interferometry, most significantly the elimination of mechanical movement of the part/s for phase modulation by implementing a tunable light source. Further, Fourier analysis on the interference time history enables this technique to accurately measure distances, treating the distance between two optical surfaces as an interferometric cavity. We propose to evaluate the uncertainty in the thickness measurement of a transparent cavity using a commercial Fizeau wavelength scanning interferometer. This work follows the theory and measurement performed in a previous manuscript of measuring absolute distances of opaque objects using a commercial wavelength scanning interferometer. The limits in measuring a cavity using the commercial wavelength scanning interferometer depend on many factors such as temperature variations that affect the test and reference cavity, uncertainty in the reference cavity calibration, tuning rate non-linearities, etc. In addition to an analytical approach, a simulation is described to better understand the measurement process and the uncertainty associated in measuring absolute distances (thickness) of cavities. Preliminary experimental results on the absolute thickness of a transparent cavity are reported along with uncertainty sources.© (2008) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.