We study the possibility of increasing the specific activity of 99Mo produced by irradiating molybdenum targets with the use of the Szilard‐Chalmers effect. According to the Szilard‐Chalmers effect, recoil atoms of the 99Mo radionuclide can be produced in nuclear reactions and retained in surrounding buffer substance. The objective of our work is to measure the yield of recoil atoms in the buffer as a function of the molybdenum layer thickness. The yield of recoil 99Mo atoms in the 100Mo(p,x)99Mo nuclear reaction as a function of metallic molybdenum nanolayer thickness has been measured. Measurements were carried out after irradiation of nanolayers in the U‐150 cyclotron with 28‐MeV protons. Nanolayers of molybdenum with thickness of 30 to 220 nm were produced by magnetron sputtering on sapphire plates. The yield of the mass of 99Mo recoil atoms was found to be the highest with the molybdenum layer thickness of 80 ± 5 nm. The enrichment factor (EF) has been defined as a ratio of the 99Mo collector specific activity (SA) to the entire target SA before separation as EF = 1200 ± 150. The specific activity of 99Mo produced in the collector was estimated to be approximately equal to 25 Ci·g−1.