Ca(2+)-binding proteins of the EF-hand family are widely expressed in the CNS, and contribute to intracellular Ca(2+) buffering in neurons. In nerve terminals, Ca(2+)-binding proteins are likely to regulate transmitter release probability and synaptic short-term-plasticity. Here, we investigated the developmental expression pattern of calretinin and parvalbumin at a large excitatory synapse, the calyx of Held in the medial nucleus of the trapezoid body (MNTB) of rats and mice. We used two-colour immunofluorescence imaging with primary antibodies detecting one of the Ca(2+)-binding proteins, and a presynaptic marker protein, Rab-3A. Calretinin was found in nerve terminals of the calyx of Held, but not in postsynaptic principal cells. The presynaptic density of Calretinin staining, and the degree of colocalization with Rab-3A increased during postnatal development (P6-P31). Surprisingly, not all calyces of Held expressed calretinin. In rats, calretinin-containing calyces were irregularly interspersed with calretinin-negative calyces, whereas in mice, calretinin-positive calyces were preferentially located in the lateral portion of the MNTB. The percentage of calretinin-positive calyces increased during development, to about 75% and 20% at P30 in rats and in mice, respectively. Parvalbumin was present in the presynaptic calyces of Held and in the nerve fibres entering the MNTB, as well as in the somata of the MNTB principal neurons. An up-regulation of calretinin and parvalbumin in calyces of Held probably increases the presynaptic Ca(2+) buffering strength during postnatal development, but the unexpected heterogeneity of calretinin expression might cause differences in Ca(2+) signalling and transmitter release probability between calyces of Held.