Objective: A common issue of freeze drying is the inhomogeneity between samples, both in regards to water content and structure. The purpose of this study is to address this issue, and try to understand the cause of inhomogeneity in the heat transfer and sample temperature. Methods: The temperature and the heat transfer was measured using different setups, both with and without vial holders at various positions at different shelf temperature and chamber pressures. By comparing sublimation rate measurements (water sample) with temperature equilibrium measurements with a non-evaporating liquid (oil sample), the heat transfer contribution from radiation and conduction could be separated and investigated individually. Results: The oil sample temperature increases each time the pressure is decreased; the increase is highest at lower shelf temperatures. Using vial holder reduces the deviation between the samples but have limited effect on the temperature increase. The sublimation rate for water sample is pressure dependent and samples close to the walls have a higher sublimation rate than vials in the center. The sublimation rate increases slightly when using a vial holder but the deviation between vials becomes more random. Conclusions: The heat transfer consists of conduction through rectified vapor and radiation from surrounding walls, about 65–75% of the heat is transferred by conduction and 25–35% by radiation under normal operational conditions. As the vial holder is also influenced by the radiation, the vial inside the holder is indirectly affected by the surrounding radiation. © 2022, The Author(s).