Endoplasmatic reticulum (ER) and mitochondria are vitally important cell organelles actively participating in neuronal growth, differentiation, death and plasticity. By using a two-photon microscopy, we imaged ER, mitochondria and active synapses in the rhythmically bursting respiratory neurons. ER consisted of continuous reticulum and isolated vesicles which were found both in the soma and in dendrites. The vesicles were either stationary or moved bidirectionally with intermittent stops and were capable to take up and to release Ca2+. ER vesicles at synapses responded with changes in luminal Ca2+ in concert with synaptic activity. Mitochondria at synapses transiently depolarized after brief periods of spontaneous and evoked synaptic activity. Closely apposing ER vesicles and mitochondria exchanged their Ca2+ bidirectionally, depending on the stimulus. About 1/3 of mitochondria and 15 % of ER vesicles were mobile and both particles slowed down their movements when they approached each other. We propose that dynamic interactions between ER vesicles and mitochondria can accomplish adequate local Ca2+ handling and energy efficiency at active synapses that is important for the maintenance of the respiratory and other neuronal functions.