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Runx1 is also expressed in the central nervous system, but little is known of its functions in brain development. At mouse embryonic day (E) 17.5, Runx1\u2010positive neurons were detected in the ventrocaudal subdivision of the hypoglossal nucleus. Runx1\u2010positive neurons lacked calcitonin gene\u2010related peptide (CGRP) expression, whereas Runx1\u2010negative neurons expressed CGRP. Expression of CGRP was not changed in\n                    <jats:italic>Runx1<\/jats:italic>\n                    \u2010deficient mice at E17.5, suggesting that Runx1 alone does not suppress CGRP expression. Hypoglossal axon projections to the intrinsic vertical (V) and transverse (T) tongue muscles were sparser in\n                    <jats:italic>Runx1<\/jats:italic>\n                    \u2010deficient mice at E17.5 compared to age\u2010matched wild\u2010type littermates. Concomitantly, vesicular acetylcholine transporter\u2010positive axon terminals and acetylcholine receptor clusters were less dense in the V and T tongue muscles of\n                    <jats:italic>Runx1<\/jats:italic>\n                    \u2010deficient mice. These abnormalities in axonal projection were not caused by a reduction in the total number hypoglossal neurons, failed synaptogenesis, or tongue muscles deficits. Our results implicate Runx1 in the targeting of ventrocaudal hypoglossal axons to specific tongue muscles. However, Runx1 deficiency did not alter neuronal survival or the expression of multiple motoneuron markers as in other neuronal populations. Thus, Runx1 appears to have distinct developmental functions in different brain regions. \u00a9 2015 Wiley Periodicals, Inc. 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