System for thermocycling of fluids in cartridges comprising a thermocycling unit in thermal contact with a first substantially planar and heat conducting wall of a cartridge, a light source for transmitting light into the interior of said cartridge through a second light transparent wall of said cartridge which is arranged substantially perpendicular to said first wall, a light detector for detecting light emerging from the interior of the cartridge through said second wall and a fluid providing unit coupled to an inlet of the cartridge for providing the cartridge with fluid and an outlet of the cartridge to drain gas when the cartridge is filled with fluid. The invention further concerns a cartridge for conducting the thermal cycling of fluids.
