Purpose This study aimed to characterize the clinical phenotype, genetic basis, and consequent immunological phenotype of a boy with severe infantile-onset colitis and eosinophilic gastrointestinal disease, and no evidence of recurrent or severe infections. Methods Trio whole-exome sequencing (WES) was utilized for pathogenic variant discovery. Western blot (WB) and immunohistochemical (IHC) staining were used for protein expression analyses. Immunological workup included in vitro T cell studies, flow cytometry, and CyTOF analysis. Results WES revealed a homozygous variant in the capping protein regulator and myosin 1 linker 2 ( CARMIL2 ) gene: c.1590C>A; p.Asn530Lys which co-segregated with the disease in the nuclear family. WB and IHC analyses demonstrated reduced protein levels in patient’s cells compared with controls. Moreover, comprehensive immunological workup revealed severely diminished blood-borne regulatory T cell (T reg ) frequency and impaired in vitro CD4 + T cell proliferation and T reg generation. CyTOF analysis showed significant shifts in the patient’s innate and adaptive immune cells compared with healthy controls and ulcerative colitis patients. Conclusions Pathogenic variants in CARMIL2 have been implicated in an immunodeficiency syndrome characterized by recurrent infections, occasionally with concurrent chronic diarrhea. We show that CARMIL2 -immunodeficiency is associated with significant alterations in the landscape of immune populations in a patient with prominent gastrointestinal disease. This case provides evidence that CARMIL2 should be a candidate gene when diagnosing children with very early onset inflammatory and eosinophilic gastrointestinal disorders, even when signs of immunodeficiency are not observed.