Lineage diversification in the vertebrate neural crest may occur via instructive signals acting on pluripotent cells, and/or via early specification of subpopulations towards particular lineages. Mesencephalic neural crest cells normally form cholinergic parasympathetic neurons in the ciliary ganglion, while trunk neural crest cells normally form both catecholaminergic and cholinergic neurons in sympathetic ganglia. In contrast to trunk neural crest cells, mesencephalic neural crest cells apparently fail to express the catecholaminergic transcription factor dHAND in response to BMPs in the head environment. Here, we show that migrating quail mesencephalic neural crest cells grafted into the trunk of host chick embryos colonise the sympathetic ganglia. While many express dHAND and form tyrosine hydroxylase (TH)-positive catecholaminergic neurons, the proportion that expresses either dHAND or TH is significantly smaller than that of quail trunk neural crest cells under the same conditions. Furthermore, the proportion of quail mesencephalic neural crest cells that is TH+ in the sympathetic ganglia decreases with time, while the proportion of TH+ quail trunk neural crest-derived cells increases. Thus, a subset of mesencephalic neural crest cells fails to express dHAND or TH in the sympathetic ganglia, while a further subset initiates but fails to maintain TH expression. Taken together, our results suggest that a subpopulation of migrating mesencephalic neural crest cells is refractory to catecholaminergic differentiation signals in the trunk. We suggest that this heterogeneity, together with local signals that repress catecholaminergic differentiation, may ensure that most ciliary neurons adopt a cholinergic fate.