During seed storage in tall silos the low layers of rape seeds are exposed to static pressure exerted by the upper layers. This may cause deformation and damage of seeds found in the lower layers and losses of biologically active compounds. The aim of this study was to simulate under laboratory conditions the actual ecosystem found in industrial plants and to evaluate the effect of not only the temperature and moisture content, but also static pressure on degradation of phytosterols contained in rape seeds in the course of storage. Changes in phytosterol levels were assessed using GC-MS. During storage in all samples of seeds (7–16% moisture content) under the adopted conditions of overpressure (20–60 kPa) and temperature (25–35 °C) the total content of phytosterols decreased by 3–57%. The smallest losses in the total phytosterol contents (3–4%) were recorded during storage of seeds with a 7% moisture content, irrespective of the applied storage temperature (25–35 °C) and overpressure variants (20–60 kPa). The greatest losses of phytosterols (43–57%) were observed during storage of seeds with a 16% moisture content at a temperature of 35 °C, while the higher the applied overpressure, the greater these losses were. The study showed that the greatest influence on sterol content during storage was increased seed moisture, and subsequently the temperature and the pressure. Experimental results also showed that for seeds with higher moisture contents (13 and 16%) an increase in storage temperature from 30 to 35 °C intensifies losses of individual phytosterols much more markedly that an increase in temperature from 25 to 30 °C. Moreover it was observed that overpressure over 20 kPa enhanced losses of investigated phytosterols.