This study reports a comprehensive survey of quasi-3 day (2.5–4.5 day period) planetary-scale waves in the low-latitude mesosphere and lower thermosphere (MLT) using the temperature observations from TIMED/SABER throughout 2002-2012. Occurrences and properties of the waves, including the eastward propagating zonal wavenumbers of 1, 2, and 3 (E1, E2, and E3) and vertical wavelengths are determined for each case. The impacts of these waves on the equatorial ionosphere are investigated by searching for the corresponding variations with the same periods and wavenumbers in total electron content (TEC) from the concurrent observations of the ground-based GPS network. For a threshold amplitude of 4 K in temperature, a total of 300 waves are identified, of which there are 186 E1, 63 E2 and 51 E3 events. The mean amplitudes and vertical wavelengths of these waves are calculated to be about 7.9 K and 34 km for the E1, 5.7 K and 29 km for the E2, and 5.1 K and 27 km for the E3, having the standard deviations of 1.5 K and 6.5 km, 0.6 K and 5.6 km, and 0.5 K and 6.7 km. Occurrences of the E1 cases are not observed to depend on season, but the large amplitude (>8 K) cases occur more often during solstices than at equinoxes. Similarly, the E2 and E3 cases are observed to occur the most often in January–February and May–August. Among these waves, 199 cases (66%) are found to have the corresponding variations in the equatorial ionosphere with amplitudes ≥4.2% relative to the mean TEC values (corresponding to 90th percentile). Most of these waves have long vertical wavelengths and large amplitudes (~3 times more than short vertical wavelength and small amplitude waves). Because no seasonal or solar cycle dependence on the frequency at which these waves have corresponding variations in the ionosphere at this TEC perturbation threshold is observed, we conclude there is no seasonal and solar cycle dependence on the propagation of such waves from the mesopause region to higher altitudes. We also identify that only 28 cases (19%) of the E1 TEC variations do not correspond to any E1 waves, which is consistent with the hypothesis that E1 waves are the primary cause of E1 TEC variations. Conditions that are favorable for 3-day waves to create ionospheric variations are present approximately 2/3 of the time. This study quantifies the importance and frequency of atmospheric quasi-3 day planetary-scale waves on the day-to-day variations of the equatorial ionosphere using a statistical, rather than case-study approach.