BACKGROUND Gc-globulin is a polymorphic protein with three phenotypes: Gc 1-1, Gc 2-1 and Gc 2-2. Deglycosylation of Gc-globulin results in a Gc-macrophage activating factor (Gc-MAF). This study investigated the potential of MAF as a tumour marker and the influence of Gc-phenotypes on serum MAF-concentrations. METHODS Gc-phenotype of 98 healthy individuals and 60 cancer patients was determined. MAF-levels of healthy individuals and cancer patients were analysed according to their Gc-phenotype using a Helix pomatia agglutinin-based ELISA. ROC curves analysed the efficiency of MAF as a tumour marker. RESULTS MAF-levels between controls and patients were significantly different (p<0.001). No phenotypic differences were found in the patients. In comparison with the controls, MAF-values were significantly lower in cancer patients carrying Gc 1-1 (p<0.01) and Gc 2-1 (p<0.001). No difference was observed in Gc 2-2 phenotype. Diagnostic accuracy of MAF as a tumour marker also demonstrated pronounced differences between Gc-phenotypes. CONCLUSIONS Gc-phenotype is a confounding factor when interpreting MAF-data. The value of MAF as a tumour marker varies according to phenotype. Future studies on MAF will have to consider the effect of Gc-phenotype.