Rescuing the ischemic penumbra from infarction is the mainstay of acute stroke therapy. However, the rescued penumbra may be affected by selective neuronal loss (SNL) and microglial activation (MA), which may hinder functional recovery and hence represent potential new therapeutic targets. Imaging them in vivo is currently attracting considerable interest, but relevant rat models are needed to underpin methods development and validation. Although striatal SNL/MA is well described following proximal MCA occlusion (MCAo), neocortical SNL/MA is still poorly characterized, yet has greater clinical relevance. This study aimed to assess the distribution and intensity of neocortical SNL and MA in a distal clip MCAo model known to cause severe neocortical ischemia. Spontaneously hypertensive rats were subjected to 45 min distal MCAo with ipsilateral common carotid artery occlusion. At day 14, post mortem SNL and MA were mapped using NeuN and OX42 immunohistochemistry, respectively. In a separate group, cerebral blood flow (CBF) was mapped during MCAo using (14)C-iodoantipyrine autoradiography. Values for SNL, MA, and CBF were obtained in the same set of anatomical ROIs covering the cortical MCA territory. Extensive SNL and MA affected the non-infarcted MCA cortex, adopting a well-defined regional distribution and a striking patchy/pseudo-columnar pattern. Regional intensities of SNL and MA were strongly inter-correlated, and also strikingly related to occlusion CBF, showing sharp rises for CBF <40%, i.e. the penumbra threshold. This rat model may be useful in providing in vitro reference for studies aiming to validate novel imaging tracers of SNL and MA in vivo.