The phenotypic distinction of magnocellular neurons (MNs) from the supraoptic (SON) nucleus is thought to be relevant to understanding of the effects of specific substances on the electrical activity of these neurons. Although the firing patterns of oxytocin (OT) and vasopressin (VP) neurons differ, they might appear the same both in vivo, and in vitro, making impracticable the phenotypic determination based solely on this feature. The recording of sustained outward rectifying potassium currents (SOR) and inward rectifying hyperpolarization activated currents (IR), presumably present in OT and absent in VP neurons, has been used to determine the phenotype of MCs. Nevertheless, this protocol clearly fails to identify the neurons that produce both peptides in equivalent concentration, i.e., the intermediate phenotype. For this reason, we aimed to analyze the confidence of the electrophysiological protocol by comparing their results with the molecular phenotype of the cells. For this purpose, we used hypothalamic slices containing the SON (200 μm) from Wistar rats (100g). Whole-cell patch-clamp was used to record currents in response to hyperpolarizing voltage steps (from -40 mV to -130 mV). I x V curves were built and the presence or absence of SOR and/or IR was used to distinguish between OT and VP neurons. At the end of the electrophysiological recordings, the cytoplasm of the neuron was sucked into the pipette and used for mRNA reverse transcription, cDNA pre-amplification and qPCR. Our results show that, from a total of 69 neurons, 20 showed a linear IxV relationship typical of vasopressinergic neurons, 48 showed IR and/or SOR current, characterizing oxytocinergic neurons, and one neuron could not be identified by its electrophysiological profile. On the other hand, the molecular analysis showed that 71% (n =49) of the phenotypes did not match the electrophysiological characterization, indicating that vasopressinergic neurons can exhibit both outward and inward rectifying currents. Moreover, 39% of the neurons were identified as intermediate in the qPCR experiments (n=27). Since the amount of cDNA collected from single cells is very small and needed to be amplified prior to the qPCR, a positive control of the pre-amplification was made to check if this process could modify the molecular phenotype of cell. For this purpose, the cDNA was amplified once for a first qPCR followed by a second amplification and another qPCR quantification. We observed that this procedure did not interfere with the molecular phenotype of the cells (n=10). In conclusion, due to the high specificity and reliability offered by RT-qPCR, we suggest that the electrophysiological protocol is not sensitive enough to be used as a single criterion to discriminate the different phenotypes of magnocellular neurons.