The study introduces scCircle-seq, a method for profiling extrachromosomal circular DNAs (eccDNAs) in single cells, revealing their diversity and complexity. scCircle-seq is validated in normal and cancer cell lines, showing that most eccDNAs vary between cells and are stochastically inherited during cell division. eccDNAs are preferentially produced from regions enriched in H3K9me3 and H3K27me3 histone marks and are induced during replication stress. The method is applied to patient-derived tumor samples, revealing cancer-specific eccDNA landscapes and a higher propensity of eccDNAs to form in amplified genomic regions. scCircle-seq is a scalable tool that can be used to dissect the complexity of eccDNAs across different cell and tissue types, expanding the potential of eccDNAs for cancer diagnostics.The study introduces scCircle-seq, a method for profiling extrachromosomal circular DNAs (eccDNAs) in single cells, revealing their diversity and complexity. scCircle-seq is validated in normal and cancer cell lines, showing that most eccDNAs vary between cells and are stochastically inherited during cell division. eccDNAs are preferentially produced from regions enriched in H3K9me3 and H3K27me3 histone marks and are induced during replication stress. The method is applied to patient-derived tumor samples, revealing cancer-specific eccDNA landscapes and a higher propensity of eccDNAs to form in amplified genomic regions. scCircle-seq is a scalable tool that can be used to dissect the complexity of eccDNAs across different cell and tissue types, expanding the potential of eccDNAs for cancer diagnostics.