Thermal disinfection system including a blood treatment apparatus comprising a hydraulic circuit for fluid transit, the hydraulic circuit having: - at least one dialysis supply line extending from a fluid inlet to a dialysis fluid supply outlet connectable with an inlet of a dialyzer; - a dialysis effluent line extending from a dialysate fluid return inlet to a drain exit, the dialysate fluid return inlet being configured to connect with an outlet of the dialyzer; - a heating unit configured to heat up a fluid, in particular water or a disinfectant solution or dialysis fluid or a mixture thereof, within the hydraulic circuit; - at least one temperature sensor (127, 127', 128) configured to provide a signal representative of a fluid temperature within the hydraulic circuit; - at least one pressure sensor configured to provide a signal representative of a local atmospheric pressure; the blood treatment apparatus comprising a control unit configured to perform a thermal disinfection procedure of the hydraulic circuit, the thermal disinfection procedure comprising at least the following steps performed by the control unit: - receiving the temperature signal from the at least one temperature sensor (127, 127', 128) and determining a measured temperature value (T fluid_mes) of the fluid within the hydraulic circuit; - receiving the pressure signal from the at least one pressure sensor and determining a measured local atmospheric pressure value (P atm); - determining a set temperature (T fluid_set) of the fluid based on the local atmospheric pressure value (P atm) to avoid boiling of the fluid within the hydraulic circuit, said set temperature (T fluid_set) being comprised between 70°C and 105°C; characterized by the fact that the thermal disinfection procedure further comprises at least the following steps performed by the control unit: - based on the determined set temperature (T fluid_set) calculating an estimated time (T est) to completion of the thermal disinfection procedure; - comparing the estimated time (T est) to completion of the thermal disinfection procedure with a reference time; - based on a comparison outcome, continuing with thermal disinfection procedure or recommending/starting a different disinfection procedure, e.g., a chemical disinfection procedure. - at least one dialysis supply line extending from a fluid inlet to a dialysis fluid supply outlet connectable with an inlet of a dialyzer; - a dialysis effluent line extending from a dialysate fluid return inlet to a drain exit, the dialysate fluid return inlet being configured to connect with an outlet of the dialyzer; - a heating unit configured to heat up a fluid, in particular water or a disinfectant solution or dialysis fluid or a mixture thereof, within the hydraulic circuit; - at least one temperature sensor (127, 127', 128) configured to provide a signal representative of a fluid temperature within the hydraulic circuit; - at least one pressure sensor configured to provide a signal representative of a local atmospheric pressure; the blood treatment apparatus comprising a control unit configured to perform a thermal disinfection procedure of the hydraulic circuit, the thermal disinfection procedure comprising at least the following steps performed by the control unit: - receiving the temperature signal from the at least one temperature sensor (127, 127', 128) and determining a measured temperature value (T fluid_mes) of the fluid within the hydraulic circuit; - receiving the pressure signal from the at least one pressure sensor and determining a measured local atmospheric pressure value (P atm); - determining a set temperature (T fluid_set) of the fluid based on the local atmospheric pressure value (P atm) to avoid boiling of the fluid within the hydraulic circuit, said set temperature (T fluid_set) being comprised between 70°C and 105°C; - receiving the temperature signal from the at least one temperature sensor (127, 127', 128) and determining a measured temperature value (T fluid_mes) of the fluid within the hydraulic circuit; - receiving the pressure signal from the at least one pressure sensor and determining a measured local atmospheric pressure value (P atm); - determining a set temperature (T fluid_set) of the fluid based on the local atmospheric pressure value (P atm) to avoid boiling of the fluid within the hydraulic circuit, said set temperature (T fluid_set) being comprised between 70°C and 105°C; characterized by the fact that the thermal disinfection procedure further comprises at least the following steps performed by the control unit: - based on the determined set temperature (T fluid_set) calculating an estimated time (T est) to completion of the thermal disinfection procedure; - comparing the estimated time (T est) to completion of the thermal disinfection procedure with a reference time; - based on a comparison outcome, continuing with thermal disinfection procedure or recommending/starting a different disinfection procedure, e.g., a chemical disinfection procedure. - based on the determined set temperature (T fluid_set) calculating an estimated time (T est) to completion of the thermal disinfection procedure; - comparing the estimated time (T est) to completion of the thermal disinfection procedure with a reference time; - based on a comparison outcome, continuing with thermal disinfection procedure or recommending/starting a different disinfection procedure, e.g., a chemical disinfection procedure.