Nowadays, many techniques are available to analyse pore size and distribution. However, these methodologies only enable us to examine microstructures or lack the capability to assess and evaluate perfusion efficiency through a porous material. For example, confocal fluorescence microscopy may be used to study the perfusion of the surface of the biomaterials,. but struggles to penetrate deep into materials, making it less effective for three-dimensional analysis. Moreover, the size and structure of the fluorescent particles used have a pivotal role in diffusion rate constants, also influencing the chemical and structural properties of the object under study. Besides, multiple measurements make the fluorophore lose its fluorescence activity due to light-induced damage (i.e. photobleaching). Modern medicine extensively used magnetic resonance imaging (MRI) to accurately and non-invasively characterise the properties of multiple biological materials. A pivotal advancement in MRI technology is the use of contrast agents, which enhance the visibility of specific tissues or structures. Among these contrast agents, deuterium oxide (D 2 O), also known as heavy water, emerged as a compelling choice for investigating diffusion and perfusion. 36 D 2 O and water have similar physical and chemical properties except for their nuclear mass, gyromagnetic ratios and spin number Hence, at high magnetic fields, deuterium is practically invisible when measuring at the proton frequency range. This contrast-enhanced acquisition strategy with D 2 O allows monitoring the signal attenuation of 1 H in MRI when administering D 2 O as an indirect measurement of diffusion. In this work, we use MRI and D 2 O (Fig. ) to accurately and non-invasively measure the passive diffusion and active perfusion properties of two biocompatible materials, CMC-based (i.e. cryogel) and PEGDA-based (i.e. hydrogel) scaffolds. We used D 2 O as a contrast agent to detect the decay in the proton signal due to the reduction of proton density from the original water contained within the scaffolds. Since there is an absence of chemical reactivity among the reagents, we can measure the scaffold properties non-destructively repeatedly. We successfully show the applicability and practicality of this strategy to study the passive diffusion (Fig. , left) of scaffolds contained in an enclosed environment with D 2 O and active perfusion (Fig. , right) of these using custom microfluidic systems (Fig. ). Furthermore, both studies demonstrated highly effective and reproducible within this easy-to-handle system setup. With these results, we expect to open a new prospective approach for diffusion and Figure : Diffusion (Eppendorf) and perfusion (4-well microfluidic chip) of biocompatible scaffolds using a pre-clinical 3 T MRI scanner. A) Schematic illustration of the experimental setup consisting of the scaffold under study (hydrogel or cryogel), heavy water, a 0.5 mL Eppendorf, a 4-well microfluidic platform, and a 3 T MRI scanner. For diffusion studies, we submerged the scaffolds (origin of the water proton signal) into the Eppendorf containing deuterium oxide (absence of signal). For perfusion studies, we enclosed the scaffolds into the microfluidic chip wells and injected deuterium oxide from the microfluidic features of this. B) Proton MRI coronal (green), sagittal (orange), and axial (blue) plane images of the 4-well microfluidic device filled with water using a T 1 -FLASH MRI sequence. The planes are directly related to the microfluidic platform represented in panel A). perfusion studies using MRI technology.