Background The serrated pathway is a distinct genetic/epigenetic mechanism of the adenoma-carcinoma sequence in colorectal carcinogenesis. Although many groups have reported the genetic-phenotypic correlation of serrated lesions (SLs), previous studies regarding the serrated pathway were conducted on patients with SLs that have heterogeneous germline genetic backgrounds. We aimed to compare pure somatic genetic profiles among SLs within identical patients with SPS as a homogenous germline background. Methods We analysed SLs from one patient with SPS (Case #1) and compared DNA variant profiles using targeted DNA multigene panels via NGS among the patient’s hyperplastic polyp (HP), three sessile serrated lesions (SSLs), and one traditional serrated adenoma (TSA), in addition to leucocytes as a germline variant, and separately analysed three SSLs and one tubular adenoma (TA) within another patient with SPS (Case #2). Results In two patients, no germline pathogenic variant was observed, and a known pathogenic variant of BRAF (c.1799T > A, p.Val600Glu) was observed in one TSA and one SSL in Case #1, while three SSLs exhibited the BRAF variant in Case #2. Further, the genetic profile of TA is consistent with the adenoma-carcinoma sequence pathway profile and distinct from that of the other SLs within the same patient with SPS. Conclusions These findings of pure somatic genetic variant profiles among SLs with identical germline genetic background support the previous results analysed among SLs with heterogeneous germline genetic backgrounds.