We describe an analysis strategy to obtain ultrasonography-matched axial dimensions of small animal eyes using the LenStar biometer. The LenStar optical low-coherence reflectometer is an attractive device for animal research due to its high precision, non-invasiveness, and the ability to measure the axial dimensions of cornea, anterior chamber, lens, vitreous chamber, and axial length. However, this optical biometer was designed for clinical applications in human eyes and its internal analysis provides inaccurate values when used on small eyes due to species-dependent differences in refractive indices and relative axial dimensions. The LenStar uses a near infrared light source to measure optical path lengths (OPLs) that are converted by the LenStar's EyeSuite software into geometrical lengths (GLs) based on the refractive indices and axial dimensions of the human eye. We present a strategy that extracts the OPLs, determines refractive indices specific for the small animal eye of interest and then calculates corrected GLs. The refractive indices are obtained by matching the LenStar values to ultrasonography values in the same eyes. As compared to ultrasounography, we found that the internal calculations of the LenStar underestimate the axial dimensions of all ocular compartments of the tree shrew eye: anterior segment depth by 6.17±4.50%, lens thickness by 1.37±3.06%, vitreous chamber depth by 29.23±2.35%, and axial length by 10.62±1.75%. Using tree shrew-specific refractive indices, the axial dimensions closely matched those measured by ultrasonography for each compartment. Our analysis strategy can be easily translated to other species by obtaining a similar paired data set using ultrasonography and LenStar, and applying our step by step procedures.