Dendritic spines receive most excitatory inputs in the neocortex and are morphologically very diverse. Recent evidence has demonstrated linear relationships between the size and length of dendritic spines and important features of its synaptic junction and time constants for calcium compartmentalisation. Therefore, the morphologies of dendritic spines can be directly interpreted functionally. We sought to explore whether there were potential differences in spine morphologies between areas and species that could reflect potential functional differences. For this purpose, we reconstructed and measured thousands of dendritic spines from basal dendrites of layer III pyramidal neurons from mouse temporal and occipital cortex and from human temporal cortex. We find systematic differences in spine densities, spine head size and spine neck length among areas and species. Human spines are systematically larger and longer and exist at higher densities than those in mouse cortex. Also, mouse temporal spines are larger than mouse occipital spines. We do not encounter any correlations between the size of the spine head and its neck length. Our data suggests that the average synaptic input is modulated according to cortical area and differs among species. We discuss the implications of these findings for common algorithms of cortical processing.