Due to the low concentrations in which 99mTc-radiopharmaceuticals are obtained (4–40 ng/ml), confirmation of the identity of these tracer agents in the European Pharmacopoeia is generally performed only indirectly by assessment of their retention times on RP-HPLC. We have investigated whether it is possible to obtain more direct proof of the identity of technetium-99m labelled radiopharmaceuticals using radio-LC-MS. As representative examples, negatively charged 99mTc-MAG3, positively charged 99mTc-Sestamibi and neutral 99mTc-ECD were used. The three technetium-99m radiopharmaceuticals were prepared in several conditions to obtain variable relative amounts of radiochemical impurities and variable concentrations of the complexes (pico- to nanomolar). The preparations were analyzed on a reversed phase C18 HPLC column using a radio-LC-MS system equipped with a time of flight mass spectrometer with electrospray ionization in positive ( 99mTc-Sestamibi, 99mTc-ECD) or negative ( 99mTc-MAG3, 99mTc-ECD) mode. For each of the studied complexes, the main peak in the radiometric channel coincided with the expected molecular ion mass of the corresponding technetium complex in the mass spectrometer channel. The relative error on the measured accurate mass was in the range of 10 ppm. The identity of several radiochemical impurities of the three technetium complexes was also confirmed or established. It is concluded that radio-LC-MS can be a sensitive aid in quality control of ‘no carrier added’ radiopharmaceuticals.