Introduction: The histo-anatomical structure of the heart is a key determinant of cardiac function. Histological staining of sectioned tissue provides high-resolution identification of cells and sub-cellular structures in two dimensions (2D). However, the sections cannot easily be projected to 3D images, as they do not represent an inherently co-registered stack. In order to develop detailed 3D representations of heart structure, spatial reintegration of serial 2D sections has been guided by additional data, such as magnetic resonance imaging (MRI) [1,2]. However, histology processing involves dehydration and re-embedding, causing significant changes in volume and shape of wax-embedded sample in comparison to the MRI images. This makes the combination of data obtained with both methods challenging. To overcome this, we introduce block-face imaging of black wax-embedded tissue as an intermediate imaging step in the processing pipeline for tissue reconstruction. Method: Briefly, rat hearts were excised after Schedule 1 killing according to the UK Home Office guidance on the Operation of Animals (Scientific Procedures) Act of 1986, and swiftly perfused via the aorta with normal Tyrode solution (mM: NaCl 140; KCl 5.4; MgCl2 1; HEPES 5; Glucose 10; CaCl2 1.8; pH 7.4). After washing, hearts were arrested using modified Tyrode containing elevated potassium (20mM), and fixed with a fast-acting Karnovsky’s fixative. For histological follow-up, hearts were embedded in black wax to improve the contrast between wax and tissue surface. Wax blocks were mounted on Leica SM2400 heavy-duty sledge-type microtome. Sections were cut at 10μm thickness, and an image of wax block surface was taken prior to each section. Images were taken with a remote-controlled Canon EOS 450D camera mounted above the sledge, equipped with a polarisation filter. The LED light was coupled to a beam-splitter in front of the camera. Suitable rotational alignment of the collection filter allowed selection of reflected (polarized) light from the topmost layer of the wax/ exposed tissue. This was used to identify the outline of tissue contained in the next section. Discussion: Detailed reconstruction of extended tissue volumes, such as whole hearts, requires a combination of imaging methodologies, ideally ranging from in vivo cine MRI, to ex vivo fixed tissue anatomical and diffusion-tensor MRI, through to histology allowing identification of cells. 3D reconstruction of histology stacks, and registration to other modalities, is aided significantly by an approach providing a set of inherently aligned images of the tissue acquired as it is serially sectioned. Block-face imaging of the wax-embedded tissue provides its consistent 3D volume, which can be used to guide spatial reconstruction of serial histology sections.