Using data of Japanese dense array of GPS receivers (GEONET) we analyzed variations of total electron content (TEC) over Japan during a period of low solar and geomagnetic activity in April–September 2008. During that time, five large earthquakes with magnitude M>6.8 occurred around the Japanese Islands. We calculated vertical TEC with time resolution of 1 h and we compared the TEC over Japan with TEC over southwestern USA. In order to detect abnormal signals, we processed daily TEC based on median and quartile of preceding 15 days. Knowing that the decisive role in the ionosphere state is performed by space weather effects, we compared the estimated TEC values with time series of the B z component of the interplanetary magnetic field (IMF), UV solar radiation, index of geomagnetic activity Dst and planetary index Kp. We have found that though the analyzed time period falls on the minimum of solar activity, the observed positive anomalies in the regional TEC correspond to fluctuations of IMF B z and to the following increase in Kp and Dst indices. Other case of ∼25% TEC increase in the duration of four days (DOY: 140–143) is, most likely, caused by increase in the solar UV radiation and coincides with growth of the global TEC. Other positive or negative abnormal TEC variations coincide with fluctuations of the global mean TEC or are of large spatial scale, i.e. much larger than the earthquake preparation zone. Therefore, it is rather difficult to find correlation between the observed anomalies and the five large earthquakes. Our results do not disprove the possibility of precursory phenomena but show the difficulties in identifying earthquake precursors in the ionosphere TEC on the background of TEC changes produced by space weather effects, even during solar minimum.