Background Rhabdomyosarcoma(RMS) is the most common soft tissue tumor in children. RMS of the oral cavity accounts for 10–12% of all head and neck RMS, and the tongue is a rare primary site. The most common pathological types of RMS include embryonal rhabdomyosarcoma and alveolar rhabdomyosarcoma, and spindle cell rhabdomyosarcoma(SRMS) is rare. Meanwhile, it has been reported in the literature that infant is a rare onset age in RMS. We review two cases of infant tongue SRMS, and analyze the clinical features, prognosis and susceptibility genes. Case presentation The clinical data of 2 infants with RMS of the tongue admitted to Beijing Children's Hospital were retrospectively collected. Both the children and their parents accepted exome-customized capture sequencing of single gene disease in peripheral venous blood, and the results were analyzed. Both cases were infants and diagnosed with lingual RMS at 3 and 5 months after birth, respectively. The pathological type were both spindle cell rhabdomyosarcoma. The maximum diameter of the tumor in case 1 was 8mm, and 23mm in case 2. The clinical TNM staging both were T1aN0M0. IRS staging of case 1 was II, and case 2 was I. They were both classified in the low risk group, and treated with surgery and chemotherapy. The regimen of chemotherapy including 4 courses of VAC(vincristine, actinomycin D, cyclophosphamide) regimen first, followed by 4 courses of VA(vincristine, actinomycin D) regimen. Case 1 was in complete remission at the latest follow-up, and case 2 suffered from relapse 10 months after stopping chemotherapy, and achieved complete remission after the multi-disciplinary treatment of chemotherapy, surgery and radiotherapy. The venous blood gene test of the two children did not find pathogenic mutation or possible pathogenic mutation related to RMS. In case 1, variants of CDK4 and BRCA1 gene, both unclear significance (possibly) related with RMS, were detected. For case 2, we found three variants of unknown significance that were (possibly) associated with RMS, including variants of TRIP13, APC, and RAD54L gene. Conclusions Infant tongue RMS is rare, the clinical manifestations of which lack specificity, and early recognition is difficult. The success and timing of local treatment are important prognostic factors. Genetic testing may be helpful for early detection of tumor susceptibility and prognosis estimation.