In the Golli-tau-eGFP (GTE) transgenic mouse the reporter gene expression is largely confined to the layer of subplate neurons (SPn), providing an opportunity to study their intracortical and extracortical projections. In this study, we examined the thalamic afferents and layer IV neuron patterning in relation to the SPn neurites in the developing barrel cortex in GTE mouse at ages embryonic day 17 (E17) to postnatal day 14 (P14). Serotonin transporter immunohistochemistry or cytochrome oxydase histochemistry was used to reveal thalamic afferent patterning. Bizbenzimide staining identified the developing cytoarchitecture in coronal and tangential sections of GTE brains. Enhanced green fluorescent protein (GFP)-labelled neurites and thalamic afferents were both initially diffusely present in layer IV but by P4-P6 both assumed the characteristic periphery-related pattern and became restricted to the barrel hollows. This pattern gradually changed and by P10 the GFP-labelled neurites largely accumulated at the layer IV-V boundary within the barrel septa whereas thalamic afferents remained in the hollows. To investigate whether this reorganisation is dependent on sensory input, the whiskers of row 'a' or 'c' were removed at P0 or P5 and the organisation of GFP-labelled neurites in the barrel cortex was examined at P6 or P10. In the contralateral region corresponding to row 'a' or 'c' the lack of hollow to septa rearrangement of the GFP-labelled neurites was observed after P0 row removal at P10 but not at P6. Our findings suggest a dynamic, sensory periphery-dependent integration of SPn neurites into the primary somatosensory cortex during the period of barrel formation.