ABSTRACT Background An increasing number of infant and follow-on formulas are enriched with probiotics and/or prebiotics; however, evidence for health effects of such enrichment in early childhood remains inconclusive. Objectives The present study aimed to assess whether the consumption of formula enriched with probiotics or prebiotics was associated with the risk of infection and allergic diseases in early childhood. Methods Analyses involved data for 8389 formula-fed children from the Etude Longitudinale Française depuis l'Enfance (ELFE) cohort. Enrichment of the formula with probiotics or prebiotics that was consumed from the age of 2–10 mo was identified by the formula ingredient list. Lower respiratory tract infection (LRTI), upper respiratory tract infection (URTI), gastrointestinal infection, wheezing, asthma, food allergy, and itchy rash were prospectively reported by parents up to the age of 5.5 y. Adjusted logistic regression models were used to assess associations between the consumption of enriched formula and risk of infection and allergic diseases. Results Aged 2 mo, more than half of formula-fed infants consumed the probiotic-enriched formula and only 1 in 10 consumed the prebiotic-enriched formula. Consumption of the Bifidobacterium lactis-enriched formula at 2 mo was associated with a lower risk of LRTI [OR (95% CI) = 0.84 (0.73–0.96)]. Consumption of the Bifidobacterium breve-enriched formula up to 6 mo was associated with a higher risk of LRTI [OR (95% CI) = 1.75 (1.29–2.38)] and asthma [OR (95% CI) = 1.95 (1.28–2.97)], whereas its consumption from 6 to 10 mo was associated with a lower risk of LRTI [OR (95% CI) = 0.64 (0.48–0.86)] and asthma [OR (95% CI) = 0.59 (0.40–0.88)]. Moreover, the consumption of Streptococcus thermophilus from 6 to 10 mo was associated with a higher risk of asthma [OR (95% CI) = 1.84 (1.29–2.63)]. No significant association was found for gastrointestinal infection, food allergy, and itchy rash. Overall, the consumption of prebiotic-enriched formula was not significantly associated with infection and allergy risk. Conclusions Associations between the consumption of probiotic-enriched formula and risk of respiratory symptoms differ according to the strain considered and consumption period. Further well-designed studies are needed to confirm these results.