Dendritic spines receive most excitatory inputs in the CNS. Recent evidence has demonstrated that the spine head volume is linearly correlated with the readily releasable pool of neurotransmitter and the PSD size. These correlations can be used to functionally interpret spine morphology. Using Golgi impregnations and light microscopy, we reconstructed 23000 spines from pyramidal neurons in layers 2/3, 4, 5 and 6 of mouse primary visual cortex and CA1 hippocampal region and measured their spine head diameters and densities. Spine head diameters and densities are variable within and across cells, although they are similar between apical and basal dendrites. When compared to other regions, layer 5 neurons have larger spine heads and CA1 neurons higher spine densities. Interestingly, we detect a correlation between spine head diameter and interspine distance within and across cells, whereby larger spines are spaced further away from each other than smaller spines. Finally, in CA1 neurons, spine head diameters are larger, and spine density lower, in distal apical dendrites (>200 microm from soma) compared to proximal regions. These results reveal that spine morphologies and densities, and therefore synaptic properties, are jointly modulated with respect to cortical region, laminar position, and, in some cases, even the position of the spine along the dendritic tree. Individual neurons also appear to regulate their apical and basal spine densities and morphologies in concert. Our data provide evidence for a homeostatic control of excitatory synaptic strength.