Vitamin D deficiency (VDD) and insufficiency (VDI) are common among exclusively breastfeeding infants. However, epidemiological evidence for the prevalence of VDD in infants during their first year of life in Taiwan has never been found. This trial determined the prevalence of VDD and VDI and the association between dietary vitamin D and vitamin D nutritional status in Northern Taiwan. A cross-sectional study was conducted on infants who returned to well-baby examinations from October 2012 to January 2014 in three hospitals: Shin Kong Wu Ho-Su Memorial Hospital, Taipei Medical University Hospital, and Shuang Ho Hospital. The specific vitamin D cut-off concentrations for VDD, VDI, and VDS are 25(OH)D3 levels ≤20, 21–29, and ≥30 (ng/mL). Overall, 481 infants’ parents completed a questionnaire comprising questions related to vitamin D nutritional status, including weekly time outdoors, breastfeeding status, anthropometric measurement, and assessment of dietary intake, including milk and complementary food. The results revealed that 197 (41%) and 212 (44%) of infants in their first year of life had VDI and VDD, respectively, by the Endocrine Society guidelines. Breastfed infants had a higher prevalence of VDI (86.1%) than did mixed-fed (51.9%) and formula-fed (38.5%) infants (p < 0.001). The prevalence of VDD was 55.4% in infants aged under six months but increased to 61.6% in infants aged over six months. Infants in the VDI and VDD groups had the same anthropometrics as those in the vitamin D sufficiency (VDS) group. Our results revealed that 25(OH)D3 had a negative correlation with the intact parathyroid hormone (iPTH) when the serum 25(OH)D3 level ≤20 ng/mL (r = −0.21, p = 0.001). The VDS group had a higher total vitamin D intake than did the VDI and VDD groups, which was mainly obtained from infant formula. Our data revealed that dietary vitamin D intake and birth season were major indicators in predicting VDD. Lower dietary vitamin D intake and born in winter and spring significantly increased the odds ratio (OR) for VDI by 1.15 (95% CI 1.09–1.20) and 2.02 (95% CI 1.10–3.70), respectively, and that for VDD by 1.23 (95% CI 1.16–1.31) and 2.37 (95% CI 1.35–4.17) without covariates adjustment, respectively. Furthermore, ORs for VDI and VDD significantly differed after adjustment for covariates. In conclusion, the prevalence of VDI and VDD were high in infants during the first year of life. Breastfeeding infants had difficulty in obtaining sufficient vitamin D from diet. In cases where the amount of sun exposure that is safe and sufficient to improve vitamin D status is unclear, breastfed infants aged below one year old are recommended to be supplemented with vitamin D.