This study investigates distinct impacts of conventional El Nino and El Nino Modoki on Malaysian rainfall anomaly during the winter monsoon. Generally, during conventional El Ninos, northern Borneo experiences significant rainfall deficit while over Peninsular Malaysia the impact is minimal. In contrast, most El Nino Modoki events favour deficit rainfall over both northern Borneo and Peninsular Malaysia. The level of impacts, particularly over northern Borneo, is higher during El Nino Modoki than conventional El Nino. The different patterns of anomalous rainfall distribution during the two types of El Nino are associated with differences in regional sea surface temperature anomalies, anomalous regional circulation and the different patterns of ascending and descending air associated with the nodes of Walker circulation over this region. However, the most prominent change is the weakening and westward shifting of the anti-cyclonic circulation over the western North Pacific region.