Introduction: Infantile hemangiomas (IHs) are the most prevalent noncancerous childhood tumors, affecting up to 10% of infants. IHs develop de novo and following excessive proliferation in the first 4–9 months; they typically degenerate spontaneously in 4–7 years. While treatment is not usually required, 10–15% of cases necessitate clinical or surgical intervention due to functional impairments. Here, we present a complicated capillary IH case, from a clinical and genetic perspective. Material and Methods: A 13-month-old patient, with free family history, presented with a cutaneous capillary-venous malformation of the thigh as well as pelvic and gluteal subcutaneous masses, resulting in urinary-bladder displacement, kidney distention, cortical thinning, pyelocaliceal dilation, and rectosigmoid displacement. Following the alleviation of the patient’s symptoms and the conduction of a percutaneous nephrostomy, Sirolimus was administered for 2 years at the recommended dose. Moreover, after clinical genetic examination and informed consent of the parents, genomic DNA was extracted from a patient’s peripheral blood sample and an analysis of whole-exon sequencing (WES) was performed. Results: Treatment was successful in diminishing the pelvic and gluteal masses, but the cutaneous malformation remained. WES revealed the heterozygous c.1416A>T:p.Q472H mutation in exon 11 of the KDR gene, that encodes kinase insert domain receptor. Conclusion: According to the clinical presentation and the results of the genetic analysis, the patient was diagnosed with segmental capillary IH, caused by a missense pathogenic variant in the KDR gene, which impairs protein function and might also be responsible for the presented subcutaneous malformations.