Recent methodological advancements of fMRI allow researchers to approach the mesoscopic regime of cortical layers and columns. This revolutionizes the ability to tackle cortical information processing within brain systems. In order to interpret the layer-dependent fMRI signal, however, the underlying laminar physiology must be understood. In this educational lecture, I will give an overview of the physiology of blood vessels within GM and discuss how this physiology affects the interpretation of layer-fMRI signal changes. I will give an overview of the corresponding fMRI analysis challenges. And finally, I will discuss how intra-cortical blood vessels can differently affect fMRI contrasts of BOLD and non-BOLD sequences.