The highly regular anatomy of the cerebellum that results from myriad genetic, environmental, and stochastic events during pre- and postnatal development is nonetheless quantitatively very different among individuals. Understanding the sources of these individual differences represents an immense challenge to those interested in the cerebellum. Here we highlight the use of new methods to dissect individual differences to their genetic sources by reviewing quantitative trait locus mapping efforts in the mouse model system. We further suggest and illustrate how to combine these methods with other modern genetic techniques to accelerate our understanding. Finally, we embed these methods in a hypothetical line of cerebellar research to illustrate the vast potential of combining complex trait analysis with a systems neuroscience perspective.