Dysregulation of mitochondrial Ca2+ homeostasis is implicated in neurodegeneration and muscular atrophy. Ca2+ entry into the mitochondrial matrix via mitochondrial Ca2+ uniporter (mtCU) complex, is regulated by the Ca2+-sensitive regulator, MICU1 either homodimerized or heterodimerized with MICU2 or MICU3. Human loss of function mutation of MICU1 has been linked to skeletal muscle (SM) myopathy, motoric impairment, fatigue, and learning difficulties. In mice, we established that neuronal MICU1 deficiency is associated with motoric and learning disabilities and motor neuron loss, and that MICU1 loss in SM leads to muscular atrophy. However, the physiological mechanisms affected by mitochondrial calcium homeostasis impairments in MICU1KO are still not clear. In the present study, we tested the hypothesis that local presynaptic calcium buffering and synaptic vesicle (SV) fusion are affected by MICU1 using neuron-specific MICU1 KO mice and culturing full body MICU1 KO E15.5 primary cortical neurons. We found WT and KO neurons with similar global cytoplasmic [Ca2+] ([Ca2+]c) responses during electrical stimulation (ES). In KO neurons, mitochondrial matrix [Ca2+] ([Ca2+]m) rise was ensued even at 50nM increase in [Ca2+]c upon low pulse (10-30) field stimulation (20V, 10Hz) and it was tightly coupled with the [Ca2+]c increase. In WT neurons, high pulse (150) field stimulation (40V, 20Hz) was required for a [Ca2+]m rise, and it was delayed behind the [Ca2+]c rise. The presynaptic local [Ca2+]c rise was attenuated by the presence of mitochondria in KO neuron but not in WT. Moreover, SV fusion was suppressed in KO neurons at all the ES parameter used, particularly, the secretory response evoked by repetitive suboptimal ES seemed to be greatly inhibited in KO neurons. Blocking reacidification of alkaline trapped vesicles by bafilomycin-A1 led to a larger maximal ES-evoked secretory response in WT than KO, suggesting that the exocytosis step is affected primarily in MICU1 KO neurons. Importantly, the ES-evoked SV fusion at the boutons lacking mitochondria was not different among WT and KO, while mitochondrial presence suppressed SV fusion immensely in KO. Thus, our results reveal the specific contributions of MICU1 in regulating synaptic secretion by modulating local Ca2+ homeostasis in neuronal processes. Our next objective is to investigate if synaptic transmission is altered at the neuromuscular junction contributing to muscular atrophy in MICU1-deficient mice.