This exploratory study investigated the influence of adding a patented, specific mixture of prebiotic oligosaccharides (scGOS/lcFOS [9:1 ratio], Danone Research) to a protein substitute suitable for infants with Phenylketonuria (PKU); PKU Anamix Infant (Nutricia).This was an 8-week open-label, single-arm, pilot intervention study in 9 infants (8-week median age) diagnosed with PKU. On study entry, infants were prescribed PKU Anamix Infant to replace an infant phenylalanine-free protein substitute without prebiotics (IPS). Blood phenylalanine concentrations were monitored and stool samples analyzed for pH/bacterial groups.PKU Anamix infant was well tolerated and accepted with no adverse events reported. Overall, plasma phenylalanine and tyrosine concentrations were maintained within target ranges throughout the study (120–360μmol/l phenylalanine, 30–100μmol/l tyrosine). All infants exhibited microbiota dominated by bifidobacteria (median 58.97% at Week 8), although no statistically significant change from baseline was observed at study endpoint. No infants showed abnormally high levels of Clostridium histolyticum/lituseburense or potentially pathogenic enterobacteriaceae at any point during the study. A significant reduction in median stool pH versus baseline was observed at Week 4 (pH reduced from 6.79 to 5.83), but this significance was not present at Week 8 (pH=6.61).PKU Anamix Infant maintains phenylalanine control in line with established IPS without prebiotics and maintains levels of bifidobacteria and lowers stool pH. In exclusively breast-fed infants the latter two factors have been associated with a reduced risk of infection and may be of particular importance in infants with PKU.