Perfluorinated compounds (PFCs) are a group of chemicals widely used for many applications. In this study PFCs were investigated in maternal blood during pregnancy (at two time points) (n = 40 and 38) and 6 months after delivery (n = 47), in cord blood (n = 33) and in blood of infants six (n = 40) and nineteen months (n = 24) after birth, and monthly in breast milk samples in Germany. Concentrations in maternal serum ranged from 0.5 to 9.4 μg/L for perfluorooctane sulfonate (PFOS) and 0.7 to 8.7 μg/L for perfluorooctanoic acid (PFOA). In cord serum, the values ranged from 0.3 to 2.8 μg/L and from 0.5 to 4.2 μg/L for PFOS and PFOA, respectively. The median results from serum at six and nineteen months of age were 3.0 and 1.9 μg/L for PFOS and 6.9 and 4.6 μg/L for PFOA, respectively. In breast milk samples, PFOS ranged from <0.03 to 0.11 μg/L (median: 0.04 μg/L), while PFOA was detected only in some samples as were all other PFCs. Overall, we found low levels of PFCs in cord sera and an increase in concentrations through the first months of infant life. Although the concentrations in breast milk were low, this intake led to a body burden at the age of six months similar to (PFOS) or higher than (PFOA) that found in adults.