Light entrains the biological clock both in adult and larval Drosophila melanogaster. The Bolwig organ photoreceptors most likely constitute one substrate for this light entrainment in larvae. Acetylcholine (ACh) has been suggested as the neurotransmitter in these photoreceptors, but there is no evidence that ACh signaling is involved in photic input onto circadian pacemaker neurons. Here we demonstrate that the putative targets of the Bolwig photoreceptors, the PDF-containing clock neurons (LNs), in the larval brain express functional ACh receptors (AChRs). With the use of GAL4/UAS driven expression of green fluorescent protein (GFP) we were able to identify LNs in dissociated cell culture. After loading with the Ca²⁺-sensitive dye fura-2 we monitored changes in intracellular Ca²⁺ levels ([Ca²⁺]_i) in GFP-marked LNs while applying candidate neurotransmitters. ACh induced transient increases in [Ca²⁺]_i at physiological concentrations. These increases were dependent on extracellular Ca²⁺ and Na⁺ and likely to be caused by activation of voltage-dependent Ca²⁺ channels. Application of nicotinic and muscarinic agonists and antagonists showed that the AChRs on cultured LNs have a nicotinic pharmacology. Antibodies to several subunits of nicotinic AChRs (nAChRs) labeled the putative contact site of the Bolwig organ axon terminals with the dendrites of LNs, as well as dissociated LNs in culture. Our findings support a role of ACh as input factor onto the LNs, and suggest that Ca²⁺ is used as a second messenger mediating cholinergic input within the LNs. Experiments using a more general GAL4/UAS driven expression of GFP showed that functional expression of nAChRs is a widespread phenomenon in peptidergic neurons.