The Madden-Julian Oscillation (MJO) is known to have a substantial impact on low frequency intraseasonal flow patterns in both hemispheres. The MJO is shown to not only affect the slowly varying component of the flow on the roughly 40 day time scale, but to significantly modulate the high frequency variability within the Southern Hemisphere (SH) as well. A simple technique is utilized which objectively isolates the linear relationship between high frequency (< 30 day) variability of various atmospheric parameters over the SH to the lower frequency MJO activity, as determined by an index of outgoing longwave radiation in the tropics. It is found that the variance of < 30 day eddy activity and temperature can be significantly enhanced or reduced over a given region, depending on the stage of the MJO life cycle. During all seasons these signals are maximized within the storm track stretching from Australia into the western South Pacific. This can be understood to be a consequence of the location of strong low latitude westerly flow near the source of tropical heating variability associated with the MJO in the vicinity of Indonesia. While some regions over the SH may have only weak mean (or composite) low frequency signals tied to the MJO, the same sectors can display significant modulation of variance within those regimes that can have a large impact on the overall synoptic scale variability.