Abstract A finite element model (FEM) of the cell-compression experiment has been developed in dimensionless form to extract the fundamental cell–wall-material properties (i.e. the constitutive equation and its parameters) from experiment force–displacement data. The FEM simulates the compression of a thin-walled, liquid-filled sphere between two flat surfaces. The cell-wall was taken to be permeable and the FEM therefore accounts for volume loss during compression. Previous models assume an impermeable wall and hence a conserved cell volume during compression. A parametric study was conducted for structural parameters representative of yeast. It was shown that the common approach of assuming reasonable values for unmeasured parameters (e.g. cell–wall thickness, initial radial stretch) can give rise to nonunique solutions for both the form and constants in the cell–wall constitutive relationship. Similarly, measurement errors can also lead to an incorrectly defined cell-wall constitutive relationship. Unique determination of the fundamental wall properties by cell compression requires accurate and precise measurement of a minimum set of parameters (initial cell radius, initial cell–wall thickness, and the volume loss during compression). In the absence of such measurements the derived constitutive relationship may be in considerable error, and should be evaluated against its ability to predict the outcome of other mechanical experiments.