Abstract The field work of recording micro-earthquakes in the southern part of the Gregory Rift and the northern part of the Western Rift (Lake George, Ruwenzori and Lake Albert) was carried out in the months of June, July and August 1968 and 1969. Data were recorded by a total of five portable automatic seismographs. The network was moved from place to place through the area. Duration of the recording at each selected site was from 5 to 10 days. Analysis of the data has given new and more precise information about epicentres and depths of earthquakes with magnitudes 1 ⩽ M⩽3 in the areas under investigation. Presence of reflected and refracted waves on the earthquake records have given some new data about the structure of the earth's crust in the southern part of the Gregory Rift. The thickness of the earth's crust is 35–37 km; the velocity of P waves is 5.8 ± 0.3 km/sec for the upper layer (thickness about 18 km) and 6.5 ± 0.3 km/sec for the intermediate layer.