A new tropical deforestation experiment has been performed, with the ARPEGE-Climat atmospheric global circulation model associated with the ISBA land surface scheme. Simulations are forced with observed monthly mean sea surface temperatures and thus inter-annual variability of the ocean system is taken into account. The local mean response to deforestation over Amazonia and Africa is relatively weak compared with most published studies and compensation effects are particularly important. However, a large increase in daily maximum temperatures is obtained during the dry season when soil water stress dominates. The analysis of daily variability shows that the distributions of daily minimum and maximum temperatures are noticeably modified with an increase in extreme temperatures. Daily precipitation amounts also indicate a weakening of the convective activity. Conditions for the onset of convection are less frequently gathered, particularly over southern Amazonia and western equatorial Africa. At the same time, the intensity of convective events is reduced, especially over equatorial deforested regions. The inter-annual variability is also enhanced. For instance, El Niño events generally induce a large drying over northern Amazonia, which is well reproduced in the control simulation. In the deforested experiment, a positive feedback effect leads to a strong intensification of this drying and a subsequent increase in surface temperature. The change in variability as a response to deforestation can be more crucial than the change of the mean climate since more intense extremes could be more detrimental for agriculture than an increase in mean temperatures.