Patients with phenylketonuria (PKU), an inborn error of phenylalanine metabolism, require consistent treatment to avoid the brain toxicity caused by hyperphenylalaninemia. The treatment consists of life-long use of a low-phenylalanine diet, which aims at decreasing hyperphenylalaninemia and maintaining blood phenylalanine concentration in a safe range. Problems with balancing diet can result in suboptimal treatment outcomes; however, recent findings suggest that genetic alteration of the transport of phenylalanine might result in an additional health burden. We assessed the effect of a common variant (rs113883650) of the LAT1(SLC7A5) gene, which encodes the main transmembrane phenylalanine transporter, on the development of overweight in 54 infants with PKU who received standard therapy and adhered well to therapeutic prescriptions, and in 55 infants with a milder disease form-the so-called mild hyperphenylalaninemia (MHP), which does not require treatment. We found that infants with PKU-carriers of the rs113883650 variant had significantly higher Body Mass Index (BMI) at 1 year compared to PKU infants without the variant (mean BMI Z-Score of +1.15 SD vs -0.15 SD, respectively; t(52) = 5.25, p = 0.00005). Conversely, no significant BMI differences were detected in the subgroups of infants with MHP (t(53) = 1.15, p = 0.25). Additionally, high BMI in infants with PKU-carriers of the rs113883650 variant positively correlated with high variability of their blood phenylalanine levels (r(52) = 0.42, p = 0.002). It should be noted that this is an observational study, which does not determine causation. Nevertheless, our findings show that the rs113883650 variant of the LAT1 gene may be a risk factor for overweight in properly treated infants with PKU. Management precautions should be taken to prevent the development of overweight and obesity.