Neuronal mosaicism describes the extent of intercellular genotypic diversity within a single human brain. This somatic variability is driven by numerous mechanisms including errors in DNA replication acquired throughout development and by the activity of endogenous retrotransposons. The study of retrotransposition in neuronal mosaicism may prove crucial to understanding the true complexity of normal and aberrant brain function. Specifically, numerous lines of evidence suggest that retrotransposition specific aspects of neuronal mosaicism may contribute to the unresolved etiology of many neurologic and neuropsychiatric disorders. Here, we describe the SLAV-Seq method, a recent advancement in the field over previous approaches used to study the diversity of LINE-1 based neuronal mosaicism at the single-cell level. We describe in detail, methodology for the isolation of single cells from bulk tissue by FACS, the amplification of single-cell genomic DNA by multiple displacement amplification (MDA), the targeted enrichment of LINE-1 somatic events, and the sequencing of the LINE-1 enriched library. Finally, we discuss methods for the quantification and analysis of the neuronal mosaicism identified by SLAV-Seq and some of the current technical limitations.