Cortisol concentrations of older children in childcare centers have been found to be higher than at home. This study focuses on infant cortisol in childcare centers throughout the first year of life, and aims to investigate whether inter-individual differences can be explained by temperament, the quality of maternal behavior, and the quality of center care. Sixty-four infants were followed for 9 months after entering care at 3 months of age. Salivary samples were taken at 10.00 h and 16.00 h in center care (in post-entry weeks 1, 2, 3, 4, 8, 12, 16, 24, and 36) and at home (in post-entry weeks 1, 24, and 36). Prior to entry, mothers completed a temperament questionnaire and the quality of maternal behavior (sensitivity and cooperation) was observed during routine bathing sessions. Subsequently, the infants were visited three times at center care to observe the quality of infant's interactive experiences with their professional caregiver. Longitudinal regression models showed that both morning and afternoon cortisol were higher in center care compared to home. Longitudinal regression models showed that infants receiving higher quality of maternal behavior displayed higher morning cortisol in center care, compared to infants receiving lower quality of maternal behavior. Higher quality of maternal behavior was also related to higher afternoon cortisol in center care, but only in infants high in negative emotionality. Center care quality was not related to cortisol. In sum, young infants show higher cortisol concentrations in center care that are related to infant temperament and quality of maternal behavior at home.