Glycine receptor (GlyR) alpha3 is involved in vision, and processing of acoustic and nociceptive signals, and RNA editing of GLRA3 transcripts was associated with hippocampal pathophysiology of mesial temporal lobe epilepsy (TLE). However, neither the role of GlyR alpha3 splicing in hippocampal neurons nor the expression of splice variants have yet been elucidated. We report here that the long (L) splice variant of GlyR alpha3 predominates in the brain of rodents. Cellular analysis using primary hippocampal neurons and hippocampus cryosections revealed preferential association of synaptic alpha3L clusters with glutamatergic nerve endings in strata granulare and pyramidale. In primary hippocampal neurons GlyR alpha3L clusters also preferred glutamatergic nerve endings while alpha3K was mainly in a diffuse state. Co-expression of GlyR beta subunit with alpha3L or alpha3K produced heteromeric receptor clusters and favoured their association with GABAergic terminals. However, heteromeric alpha3L was still more efficient than heteromeric alpha3K in associating with glutamatergic nerve endings. To give physiological relevance to these results we have finally analysed GlyR alpha3 splicing in human hippocampus obtained from patients with intractable TLE. As up-regulation of alpha3K occurred at the expense of alpha3L in TLE patients with a severe course of disease and a high degree of hippocampal damage, our results again involve post-transcriptional processing of GLRA3 transcripts in the pathophysiology of TLE.