Microthermometry and laser Raman microprobe results show that aqueous inclusions in two generations of apatite from the Sukulu carbonatite, Uganda, consist essentially of three groups: CO2-bearing, moderate to high-salinity H2O-rich and CH4-bearing. The CO2- and CH4-bearing inclusions, in general are never present together in individual apatite crystals. It is considered that these compositionally discrete inclusions represent different fluids trapped during different stages of apatite crystallisation. The CO2-bearing fluid might have been formed from an originally H2O-rich fluid containing significant CO2 by immiscible separation under high pressure and temperature. This precursor H2O-CO2 fluid was probably derived from a carbonatite melt, also by a possible process of liquid immiscibility. The CH4-bearing inclusions were probably formed by late-stage hydrothermal processes under different P-T conditions. P-T-X isochores calculated for each type of fluid indicate that the evolution of the fluids in the system might be from a CO2-bearing, through moderate to highly saline, to CH4-bearing stages, under physical conditions varying from high, through moderate P and T, to low P. This trend may be applied in interpreting the evolution of the carbonatite from a deep magmatic (carbonate melt) environment towards a shallow level hydrothermal system. The three types of fluid inclusions, together with Mg-calcite inclusions in the apatite crystals, indicate that the compositions of the fluids associated with the Sukulu carbonatite complex appear to have evolved chemically from a Mg-bearing calcite melt, through aqueous CO2-bearing and bicarbonate-rich melts (NaHCO3 daughters) to a final aqueous CH4-bearing fluid.