The aim of this study was to evaluate the morphology of the stapedius muscle and its tendon with the use of microCT and to describe their anatomic relationship with facial nerve and incudostapedial joint. The study was performed on 16 fresh cadaveric temporal bones scanned in microtomography (microCT). Stapedius muscle and its tendon were identified in each set of images. The length of the medial and lateral border of the stapedius tendon (STL-med, STL-lat), width at the insertion to stapes (STW-s), at the point it emerges from the pyramidal eminence (STW-p) and in the half way from the pyramidal eminence to stapes (STW-m), and the length and the width of the belly of stapedius muscle (BSML and BSMW) were measured in modified axial plane. The shortest distance between the facial canal and incudostapedial joint (FN-isj), and between the facial canal and stapedius tendon (FN-st) were measured in the Pöschl plane. The average values of all distances measured were: STL-lat 1.29 ± 0.50 mm, STL-med 1.27 ± 0.44 mm, BSML 2.98 ± 0.51 mm, STW-s 0.47 ± 0.10 mm, STW-p 0.46 ± 0.12 mm, STW-m 0.35 ± 0.12 mm, BSMW 1.26 ± 0.29 mm, FN-isj 1.72 ± 0.33 mm, FN-st 1.35 ± 0.30 mm. The stapedius muscle complex consists of the tendon and the belly, and the border between them in microCT scans is not always evident. The distance between the facial nerve and the incudostapedial joint is greater than the distance between the facial nerve and the stapedius muscle tendon.