Although mast cells are immune cells of hematopoietic origin, they can be found in parts of the central nervous system of many mammalian species. In the rat brain they are located in the thalamic region. Their function is not defined yet, although they are mostly known to secrete several chemicals, which may influence the surrounding neurons. There are no in vivo electrophysiological data available on the possible effects of brain mast cells on neurons. In this study, we used a combined method of microiontophoresis and extracellular single unit recording to simultaneously activate mast cells and record neuronal action potentials. Four-barrelled micropipettes were used for recording neuronal activity and for microiontophoretic application of mast cell degranulator Compound 48/80 (C48/80). Spike sorting routines were performed on-line and off-line to ensure that data were always recorded from a single neuron. C48/80 did not modify the firing rate of cortical neurons (no mast cells are found there), however, it caused excitation (n = 16/37, 43%), or inhibition (n = 9/37, 24%) in thalamic neurons possibly due to mast cell activation. Further investigations will clarify the biochemical nature of changes in neural excitability due to mast cell degranulation in the mammalian brain.