Rubia cordifolia has been used to treat diseases for many years in China and India. Although the biological properties and major compounds of R. cordifolia have been extensively studied, the underlying mechanisms of its biological effects remain elusive. In terms of immunological effects, anti-inflammation effect of macrophage (Raw 264.7) simply has been reported. In this study, R. cordifolia was extracted in 70% ethanol and the extract did not affect to macrophage (Raw 264.7) pro-inflammation and T cell (Molt-4). However, in mast cell (RBL-2H3), it showed inhibition of degranulation. The inducing inhibitory effect on degranulation was related to concentration dependent variation in phosphorylation of ERK-1/2 and upregulating the JNK phosphorylation in RBL-2H3 cells. Based on these data, we concluded that R. cordifolia newly have anti-allergenic effects in RBL-2H3 and might be used as a therapeutic agent to treat or prevent allergic diseases such as asthma and atopic dermatitis.