Background: This paper determined the morphometric measurements of the brainstem including mesencephalon, pons and medulla using magnetic resonance imaging (MRI) in Turkish healthy population. Materials and methods: Two hundred sixty-three (263; 158 females and 105 males) subjects aged from 18 to 65 years were included in this study. The measurements were taken from subjects having brain MRI in the Radiology Department. Statistical analysis was done by SPSS 21.00 package programme. ANOVA test and χ2 test were used to determine the relation between measurements and age and sex groups. The p < 0.05 value was considered as significant. Results: The overall means and standard deviations of the measurements were: pons anteroposterior diameter, 15.41 ± 1.27 mm; pons vertical diameter, 22.02 ± 2.07 mm; mesencephalon anteroposterior diameter 9.39 ± 1.00 mm; mesencephalon vertical diameter, 15.20 ± 1.53 mm; distance between the interpeduncular fissure and aqueduct, 11.72 ± 1.58 mm; distance from cerebral peduncles to aqueduct, 13.64 ± 1.66 mm; anterior surface of the pons midway between the mesencephalon and medulla to the fourth ventricular floor, 21.62 ± 1.64 mm; the shortest anteroposterior diameter of the medulla at the pontomedullary junction, 13.46 ± 1.28 mm, and the shortest anteroposterior diameter of the medulla at the medullospinal junction, 10.24 ± 1.43 mm in females, respectively, whereas the corresponding values were 15.58 ± 1.53 mm; 22.64 ± 2.35 mm; 9.37 ± 1.66 mm; 15.64 ± 1.52 mm; 11.14 ± 1.31 mm; 13.01 ± 1.30 mm; 21.97 ± 1.65 mm;13.47 ± 1.19 mm; 9.91 ± 1.35 mm in males, respectively. There were significant differences in some parameters such as pons vertical diameter, mesencephalon vertical diameter, distance between the interpeduncular fissure and aqueduct, and distance between cerebral peduncles to aqueduct between sexes. Conclusions: The brainstem dimensions of healthy population provide important and useful knowledge in terms of comparison of abnormalities clinically. These data may be valuable for the representatives of clinical disciplines. (Folia Morphol 2020; 79, 1: 36–45)