[Background]Recent studies have shown that prenatal exposure to perfluorinated compounds (PFCs) at general environmental levels has an adverse effect on infants. Immunotoxic effects of PFCs exposure in animal studies include immunosuppression, suppression of IgM antibody production, and increased IgE response in ovalbumin-sensitized mice. However, epidemiological studies investigating the role of PFCs, in particular longer-chain PFCs, are scarce. [Aims]The aim of this study was to investigate the relationship between prenatal exposure to 11 PFCs and infant allergic diseases during the first 12 months of life in a large study population. [Methods]The study population was comprised of mothers and their infants enrolled in a prospective birth cohort study (Hokkaido Study on Environment and Children's Health). Between February 2003 and December 2009, 300 women were randomly selected every year. Eleven PFC compounds were measured in maternal plasma using simultaneous analysis with UPLC-MS/MS. Characteristics of participants and information on infant allergic diseases was obtained from self-administered questionnaires and medical records. Finally, 2,062 mothers and their infants were included in the statistical analysis. [Results]Risk of eczema, wheezing and food allergy during the first 12 months of life was not associated with maternal levels of 11 PFCs, including longer-chain compounds. Odds ratios for eczema and wheezing ranged from 0.66 to 0.73 and from 0.60 to 0.81 for the three higher quartiles of maternal perfluorotridecanoic acid (PFTrDA) levels, compared with the lowest in the adjusted models, but no dose-response pattern was found. [Conclusions]These findings suggest that prenatal exposure to 11 PFCs, including longer-chain compounds, is not associated with risk of infant allergic diseases. Further studies are ongoing to investigate the effects of prenatal exposure to 11 PFCs on cord blood IgE levels, and allergies and infectious diseases at the age of 2 and 4 years.