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Abstract In the past decade, there has been major interest in understanding the role of transcriptomics in the functional and anatomical layout of the human brain. To date, almost all of the work linking transcriptomics to human brain function and structure has been restricted to the cerebral cortex. The culmination of this work has identified transcriptomics as an important shared principle that can tie together function, structure, and gene expression. However, largely missing from this work is the subcortex—namely the cerebellum. Here, we investigate whether transcriptomics offer a link between function and structure in the human cerebellum, using gene expression data from post-mortem cerebella and multi-modal brain atlases. We find that transcriptomic gradients from a sparse subset of genes align with a macroanatomical, rather than a functional - parcellation of the cerebellum, and the transition of the main gradient occurs at the horizontal fissure for the group, as well as individual cerebella. Conversely, when filtering for cortex-specific genes, there is an alignment with continuous functional gradients of the cerebellum, but not discrete parcellated areas.