Objectives: To set age-specific normal reference values for brainstem, cerebellar vermis, and peduncles measurements and characterize values' variations according to gender, age, and age by gender interaction. Methods: 565 normal brain magnetic resonance examinations with normal anatomy and signal intensity of the supra- and infratentorial structures were categorized into six age groups (infant, child, adolescent, young adult, middle-age adult, and old aged adults). Patients with congenital malformations, gross pathology of the supra- or infratentorial brain, brain volume loss, developmental delay, metabolic disorders, and neuropsychological disorders (n = 2.839) were excluded. On midsagittal T1 weighted and axial T2 weighted images specific linear diameters and ratios of the brainstem, cerebellar vermis, and peduncles were attained. Two observers assessed a random sample of 100 subjects to evaluate the inter- and intraobserver reproducibility. Intraclass correlation coefficients, means ± standard deviation, one and two-way analysis of variance tests were used in the statistical analysis. Results: Good to excellent inter- and intraobserver measurements' reproducibility were observed, except for the transverse diameter of the midbrain, the anteroposterior diameter of the medulla oblongata at the pontomedullary and cervicomedullary junctions, cerebellar vermis anteroposterior diameter, and thickness of the superior cerebellar peduncle. Age-specific mean values of the investigated measurements were established. A significant gender-related variation was recorded in the anteroposterior diameter of the basis pontis (p = 0.044), the anteroposterior diameter of the medulla oblongata at the cervicomedullary junction (p = 0.044), and cerebellar vermis height (p = 0.018). A significant age-related change was detected in all measurements except the tectal ratio. Age by gender interaction had a statistically significant effect on the tectal ratio, inferior, and middle cerebellar peduncles' thickness (p = 0.001, 0.022, and 0.028, respectively). Conclusion: This study provides age-specific normal mean values for various linear dimensions and ratios of the posterior fossa structures with documentation of measurements' variability according to gender, age, and their interaction. Advances in knowledge: It provides a valuable reference in the clinical practice for easier differentiation between physiological and pathological conditions of the posterior fossa structures especially various neurodegenerative diseases and congenital anomalies.