Purpose: Patients with schizophrenia or bipolar disorder are at increased risk of somatic illnesses and have more somatic complaints compared with the general population. Schizophrenia and bipolar disorder are highly heritable. Already during childhood, children at familial high risk of schizophrenia (FHR-SZ) or bipolar disorder (FHR-BD) are at increased risk of psychiatric disorders and cognitive and social impairments. Knowledge about physical conditions is sparse.Materials and methods: Through blood tests (n = 293), interviews, and questionnaires, we assessed inflammatory markers, somatic complaints, medication - and health care use in 11-year-old children at FHR-SZ, FHR-BD, and population-based controls (PBC).Results: Children at FHR-SZ had higher concentrations of leucocytes (mean 6.41, SD 0.73) compared with PBC (mean 5.78, SD 0.27, p = 0.005) and of neutrophilocytes (FHR-SZ: mean 3.11, SD 1.32, PBC: mean 2.70, SD 0.96, p = 0.024). Compared with PBC (26.6%), more children at FHR-SZ (40.5%, p = 0.007) reported somatic complaints. So did caregivers and teachers to children at FHR-BD. Somatic complaints, higher concentrations of leucocytes, and neutrophilocytes were associated with lower levels of physical activity. Children at FHR-BD with psychiatric disorders reported more somatic complaints compared with those without.Conclusion: Children at FHR-SZ had higher concentrations of leucocytes and neutrophilocytes than PBC. Children at FHR-SZ or FHR-BP displayed more somatic complaints than controls. Our study highlights rarely explored disadvantage of being born to parents with schizophrenia or bipolar disorder. To enhance understanding of how physical conditions in childhood may interplay with later transition to mental disorders in children at FHR-SZ and FHR-BD, further research is needed.