Exercise leads to symptom reduction in affective disorders and functional somatic syndromes. Biological hypotheses of underlying mechanisms include serotonergic and immunological pathways. We aimed to investigate biological features in persons with major depression and somatoform syndromes, and to analyze effects of short-term graded exercise on these parameters. Baseline values for depressive and somatoform symptoms, tryptophan, kynurenine, 5-hydroxyindoleacetic acid, neopterin and interleukin-6 were compared with those after one week of increased and one week of reduced physical activity. Thirty-eight persons with major depression, 27 persons with a minimum of 6-8 somatoform symptoms, and 48 healthy controls participated in the study. Depressive and somatoform symptoms were reduced after the active week, and an interaction pointed towards group-specific reduction of psychopathology. Participants with major depression had lower levels of kynurenine compared to controls, with intermediate concentrations in somatoform patients. There were no systematic associations of symptom improvement with biological changes. A possible limitation of the design is that a control condition with low physical activity, but no placebo condition was included. People with multiple somatoform symptoms and major depression benefit from a short and low-graded exercise intervention. These effects do not seem to be mediated by changes in serotonergic and inflammatory parameters.