This cross-sectional study assessed vitamin D status of healthy infants and young children undergoing routine care in a medical center pediatric clinic in Sacramento, CA, and evaluated associations of status with markers of vitamin D function. Such data have not recently been reported from similar locations with sunny climates that should minimize risk of deficiency. Exposures included diet, supplement use, and sun exposure, and outcomes included plasma 25-hydroxy vitamin D (25[OH]D), parathyroid hormone (PTH), bone-specific alkaline phosphatase, and eight markers of immune activation. The median age of the 173 subjects was 12 months (range, 6–19); 49% were female. The median 25(OH)D was 85 nmol/l (range, 9–198); five subjects (2.9%) had <27.5 nmol/l, indicative of deficiency; 14 (8.1%) had <50 nmol/l, and 49 (28.3%) had <75 nmol/l. Most subjects (154; 89%) received some vitamin-D-fortified cow’s milk or formula while 19 (11%) received breast milk as the only milk source. Breastfeeding was associated with risk of vitamin D deficiency (p < 0.001). Subjects with 25(OH)D <27.5 nmol/l had elevated PTH (p = 0.007). Only four of 35 breastfed infants (11%) consuming <500 ml/day vitamin-D-fortified formula or milk received vitamin D supplements. Plasma interleukin (IL)-1β was significantly higher (p = 0.036) in infants in the highest vs. lowest 25(OH)D decile. In conclusion, this study demonstrates that vitamin D deficiency with elevated PTH remains a risk for breastfed subjects not receiving supplemental vitamin D even in a region with a sunny, temperate climate. Strategies to improve supplementation should be sought.