The ability to estimate durations varies across individuals. Although previous studies have reported that individual differences in perceptual skills and cognitive capacities are reflected in brain structures, it remains unknown whether timing abilities are also reflected in the brain anatomy. Here, we show that individual differences in the ability to estimate subsecond and supra-second durations correlate with gray matter (GM) volume in different parts of cortical and subcortical areas. Better ability to discriminate subsecond durations was associated with a larger GM volume in the bilateral anterior cerebellum, whereas better performance in estimating the suprasecond range was associated with a smaller GM volume in the inferior parietal lobule. These results indicate that regional GM volume is predictive of an individual's timing abilities. These morphological results support the notion that subsecond durations are processed in the motor system, whereas suprasecond durations are processed in the parietal cortex by utilizing the capacity of attention and working memory to keep track of time.