Background: Infantile colic is a common condition with limited knowledge about later clinical manifestations. We evaluated the role of the early life gut microbiome in infantile colic and later development of atopic and gastrointestinal disorders. Methods: Copenhagen Prospective Studies on Asthma in Childhood₂₀₁₀ cohort was followed with 6 years of extensive clinical phenotyping. The 1-month gut microbiome was analyzed by 16S rRNA sequencing. Infantile colic was evaluated at age 3 months by interviews. Clinical endpoints included constipation to age 3 years and prospectively diagnosed asthma and atopic dermatitis in the first 6 years of life, and allergic sensitization from skin prick tests, specific Immunoglobulin E, and component analyses. Results: Of 695 children, 55 children (7.9%) had infantile colic. Several factors were associated with colic including race, breastfeeding, and pets. The 1-month gut microbiome composition and taxa abundances were not associated with colic, however a sparse Partial Least Squares model including combined abundances of nine species was moderately predictive of colic: median, cross-validated AUC = 0.627, p =.003. Children with infantile colic had an increased risk of developing constipation (aOR, 2.88 [1.51–5.35], p =.001) later in life, but also asthma (aHR, 1.69 [1.02–2.79], p =.040), atopic dermatitis (aHR, 1.84 [1.20–2.81], p =.005) and had a higher number of positive allergic components (adjusted difference, 116% [14%–280%], p =.012) in the first 6 years. These associations were not mediated by gut microbiome differences. Conclusions: We link infantile colic with risk of developing constipation and atopic disorders in the first 6 years of life, which was not mediated through an altered gut microbiome at age 1-month. These results suggest infantile colic to involve gastrointestinal and/or atopic mechanisms.