Purpose A 3D printer was used to realise compartmental dosage forms containing multiple active pharmaceutical ingredient (API) formulations. This work demonstrates the microstructural characterisation of 3D printed solid dosage forms using X-ray computed microtomography (X mu CT) and terahertz pulsed imaging (TPI). Methods Printing was performed with either polyvinyl alcohol (PVA) or polylactic acid (PLA). The structures were examined by X mu CT and TPI. Liquid self-nanoemulsifying drug delivery system (SNEDDS) formulations containing saquinavir and halofantrine were incorporated into the 3D printed compartmentalised structures and in vitro drug release determined. Results A clear difference in terms of pore structure between PVA and PLA prints was observed by extracting the porosity (5.5% for PVA and 0.2% for PLA prints), pore length and pore volume from the X mu CT data. The print resolution and accuracy was characterised by X mu CT and TPI on the basis of the computer-aided design (CAD) models of the dosage form (compartmentalised PVA structures were 7.5 +/- 0.75% larger than designed; n = 3). Conclusions The 3D printer can reproduce specific structures very accurately, whereas the 3D prints can deviate from the designed model. The microstructural information extracted by X mu CT and TPI will assist to gain a better understanding about the performance of 3D printed dosage forms.