Antisense oligodeoxynucleotides (ODNs) have the potential to be a powerful tool for regulating gene expression and mRNA translation in spatially and temporally restricted domains. Prior to investigating the effects of antisense ODNs on hippocampal long-term potentiation, we investigated whether there are any non-specific effects of ODNs on perforant path synaptic transmission in the dentate gyrus of both pentobarbital-anaesthetized and awake, freely moving rats. Single injections of phosphorothioated antisense ODNs (4 nmol) to the immediate early gene zif/268 caused a rapid (within minutes) and long-lasting (>24 hr) profound depression of the perforant path evoked field potentials. This depressive effect was due to the phosphorothioate modification since a depression was not seen with unmodified antisense ODNs, relative to saline controls. Furthermore, the effect was not sequence-specific since modified sense ODNs caused the same degree of depression. The depression caused by the modified antisense ODNs was dose-dependent and specific to synaptic transmission, since antidromic population spikes elicited by mossy fibre stimulation were relatively unaffected compared to the orthodromic responses. A second unexpected side-effect of the modified ODNs was cellular hyperexcitability, such that bursts of epileptiform spikes in the EEG occurred both spontaneously and as a result of synaptic stimulation. While the mechanism of the synaptic depression remains unknown, these results indicate that phosphorothioate-modified ODNs exert profound non-specific effects on synaptic transmission in the hippocampus, that have the potential to seriously compromise any corresponding behavioural or electrophysiological studies.