Gray matter heterotopia (GMH) is caused by malformation of cortical development, which exhibits as gray matter nodules abnormally located within the white matter region, and most GMH patients have concomitant epilepsy. Although antiepileptic drugs can control seizures, over 40% of patients still require surgery to pursue a cure for the disease. Previous researchers have studied GMH from the genetic perspective, and several disease-specific gene modifications were identified to elucidate the pathogenesis.1 However, to acquire a deeper understanding of the disease progression, it is essential to comprehensively explore the transcriptional alterations caused by GMH. Here, we sought to analyze the cell types and their distinct transcriptional changes in GMH. Thus, we studied the lesional tissues from GMH patients using single-cell RNA sequencing, which captured the cell-type specific transcriptome at single-cell resolution.