Abstract: The neurophysiological effects induced by emotional background during meditation and the associated gender differences were investigated. Event-related potentials (ERPs) were recorded in 52 young adults listening to positive and negative meditative guidance programs. A fixed-frequency D-like sound was used as a cue to evoke ERPs. The main ERP components induced by a fixed-frequency sound were N2 and P3 components, observed temporally at N160 and P240, respectively. These two components serve as the markers for exploring stimulus differences and attention resource allocation, respectively. More negative N160 amplitude and reduced P240 amplitude were observed in the prefrontal cortex (PFC) under the positive meditation (PM) condition than under the negative meditation (NM) condition. Significant gender differences in ERP responses were also found, preferentially in the NM condition, with a more pronounced difference of frontal lateralization between the NM and PM conditions. The N160 amplitude of the left frontal lobe in men is significantly greater than that of the right frontal lobe; the P240 amplitude of the right frontal lobe in women is significantly larger than that of the left frontal lobe. These findings proved that positive guidance and negative guidance can affect the emotional regulation effects of meditation differently and there is also a gender difference in the neurophysiological effects of meditation.