Characteristics of the ‘stochastic’ component of atmospheric variability that is uncoupled from the slowly varying tropical ocean are detailed. The stochastic components of tropical convection and surface zonal wind display a distinct peak in their power spectra at global wavenumbers 1-2 for periods 30-90 days, characteristic of the Madden-Julian Oscillation (MJO). Forcing a linear shallow water model with the tropcially coherent zonal stress reveals efficient generation of equatorial Kelvin waves with a period of approximately 70 days. The seasonality present in the stochastic zonal stress is transmitted to the eastern Pacific thermocline variability by these Kelvin waves. During an El Niño event, the stochastic zonal stress variance shifts eastwards from the western Pacific along with the large-scale surface westerly winds and warm sea surface temperatures (SSTs). Hence, the noise is a function of the state of El Niño. A low frequency warming in SST is also related to the thermocline suppression in the eastern Pacific Ocean generated by eastward propagating westerly winds over the western Pacific 2 months earlier. The stochastic zonal stress also exhibits weak westerly anomalies in the western Pacific some 6-8 months prior to El Niño, which perhaps explains why observed El Niño variability is recovered when weakly damped models are forced with similar estimates of observed stochastic zonal stress.