Rapid acquisition of volumetric data is a mandatory prerequisite for small animal in vivo imaging. Due to its high sensitivity and capacity to extract the sample depth profile in parallel Fourier Domain Optical Coherence Tomography (FDOCT) complies with this requirement. The absence of labeling further simplifies its use for in vivo application. In order to provide the high spatial resolution necessary to gain biologically relevant insights focusing optics from microscopy are usually employed. The resulting focal spot however has a limited depth of field and compromises with imaging speed and parallel depth extraction. Using a Bessel‐like illumination beam, obtained by use of a conical lens, and detection optics with a low numerical aperture, we achieve a compromise between high lateral resolution and extended depth of field and obtain near isotropic resolution. Together with a scanning system deflecting the beam rapidly in the lateral directions and a fast signal acquisition and processing routine this extended focus Optical Coherence Microscope (xfOCM) was used to measure murine islets of Langerhans. These endocrine islets are assemblies of insulin secreting beta cells contained within the exocrine tissue of the pancreas. Assessing the structure and function of individual islets is important to further the understanding of diabetes’ mechanisms. In this work we used xfOCM to measure islets, pancreatic lobules, ducts and blood vessels, first in excised tissue, and then we demonstrate the potential of this method with volumetric measurements of the pancreatic islets in vivo and in situ.