Efforts to identify biological correlates of internalizing symptoms in childhood have involved examinations of HPA-axis functioning, namely Cortisol Awakening Response (CAR). However, research has not assessed the relationship between CAR and internalizing problems among children younger than 8 years. Findings with older samples have been somewhat equivocal, perhaps due to high rates of co-occurring externalizing symptoms during childhood and/or due to age-related differences. This cross-sectional study examined CAR in an at-risk sample of children aged 22 months to 8 years at various levels of risk for internalizing symptoms. Internalizing symptoms were associated with blunted CAR, but only after controlling for externalizing problems. The relationship between CAR and internalizing symptoms disappeared with age. Results demonstrate that a negative association between CAR and internalizing exists during early childhood and illustrate the importance of accounting for comorbid externalizing disorders and developmental stage when assessing the HPA-internalizing link.