Specimen-induced aberrations affect the imaging properties in optical 3D microscopy, especially when high numerical aperture lenses are used. Studies on aberrations are often properly concerned with the degradation of image quality such as compromised resolution or reduced signal intensity. Apart from these, aberration effects can also introduce geometric image distortions. The effects, discussed here are particularly strong when thick biological specimens are investigated. Using a high numerical aperture interferometer, we measured wavefront aberrations in transmission mode and quantified geometric distortions associated with specimen-induced aberrations. This assessment for a range of biological specimens allows estimation of the accuracy of spatial measurements. The results show that high-resolution spatial measurements can be significantly compromised by specimen-induced aberrations.