Aim Our previous result showed that at the concentration of 25 mg/(kg.d), Momordicin has a distict therapeutic effect on coxsackievirus B3 (CVB3) viral myocarditis. Because nuclear factor kappa B (NF κB) is Key tactor in immunity and inflammatory reaction, we measure the regulation effect of Momordicin to the level of NF κB. Method To purified Momordicin from Momordica as our previous report, 5 groups of animal are used in this experiment: control of virus group (VC group); control of normal group (NC group); control of Momordicin group (MC group); low dose Momordicin therapeutic group (LM group); high dose monordicin therapeutic group (HM group). Animals were killed at 0 d, 3 d, 7 d, 14 d and 21 d, and purified nucleus protein, protein quantifyed by BCA method, then measuring the activity of EMSA and assys the result. Result The activity of NF κB are still measuerable in the DC group at 21 d, and it's activity is higher than the NC group; there are different degree of inhibition effect in HM and LM groups to NF κB activity, and nerely no NF κB was appeared in the HM and MC groups; there are low level NF κB acitivity were found in the NC group. Conclusion The curing effect of momordicin to viral myocarditis may related to it's inhibitory effect to NF κB activity.