Amide proton transfer (APT) MRI is assumed to report on the intracellular environment. However, no attempt has been made to verify this assumption, or examine the extent to which tissue compartmentalisation contaminates measurements of biophysical parameters (e.g. protein concentration, pH) from APT MRI data. In this simulation study, we show that measurement of biophysical parameters by APT MRI is influenced by tissue compartmentalisation when the transcytolemmal exchange rate is slow (<2Hz). Since recent studies have reported transcytolemmal exchange to be in such a regime, it may be possible to separate intra- and extracellular APT signals.