Non-technical summary The sizes of neurons and their synaptic connections are regulated by multiple molecular mechanisms to provide neuronal networks that perform well-defined functions. Deletion of the tumour suppressor phosphatase and tensin homologue deleted on chromosome ten (PTEN) during early development leads to a 2-to 3-fold increase in neuronal and synaptic size and abnormalities in synaptic plasticity, the cellular mechanism underlying learning and memory. Whether PTEN deletion affects synaptic plasticity directly or as a consequence of its effect on the neuronal and synaptic size remained unclear. Here we show that deletion of the Pten gene in mice during postnatal development, when the central nervous system is formed, does not affect neuronal or synaptic size but impairs synaptic plasticity. Thus, PTEN affects neuronal structure and synaptic plasticity through independent mechanisms. Abstract The tumour suppressor PTEN is the central negative regulator of the phosphatidylinositol 3-kinase (PI3K) signalling pathway, which mediates diverse processes in various tissues. In the nervous system, the PI3K pathway modulates proliferation, migration, cellular size, synaptic transmission and plasticity. In humans, neurological abnormalities such as autism, seizures and ataxia are associated with inherited PTEN mutations. In rodents, Pten loss during early development is associated with extensive deficits in neuronal migration and substantial hypertrophy of neurons and synaptic densities; however, whether its effect on synaptic transmission and plasticity is direct or mediated by structural abnormalities remains unknown. Here we analysed neuronal and synaptic structures and function in Pten-conditional knockout mice in which the gene was deleted from excitatory neurons postnatally. Using two-photon imaging, Golgi staining, immunohistochemistry, electron microscopy, and electrophysiological tools, we determined that Pten loss does not affect hippocampus development, neuronal or synaptic structures, or basal excitatory synaptic transmission. However, it does cause deficits in both major forms of synaptic plasticity, long-term potentiation and long-term depression, of excitatory synaptic transmission. These deficits coincided with impaired spatial memory, as measured in water maze tasks. Deletion of Pdk1, which encodes a positive downstream regulator of the PI3K pathway, rescued Pten-mediated deficits in synaptic plasticity but not in spatial memory. These results suggest that PTEN independently modulates functional and structural properties of hippocampal neurons and is directly involved in mechanisms of synaptic plasticity.