Where the evidence is strongest: asthma and obesity
The most consistent and concerning finding across these studies is that antibiotics in the first two years of life are linked to a higher risk of childhood asthma and obesity. This isn't a small effect. A 2025 systematic review that specifically looked at studies designed to rule out bias found that even after accounting for the fact that sick kids get more antibiotics, the risk of asthma remained 19% higher (pooled odds ratio 1.19) [9]. Another massive study of over 33,000 children found that antibiotic exposure in the first 24 months increased the risk of obesity by 20% (hazard ratio 1.20) [2]. The same study showed that antibiotics given during pregnancy or at birth had no such effect, pointing to a critical window in infancy [2].
The link to asthma gets stronger the more antibiotics a child receives. A Danish study of nearly a million children found that while any antibiotic in the first year raised Crohn's disease risk by 40%, the risk jumped to 4-fold for children who had six or more courses [4]. For asthma, a large Australian study found that any early-life antibiotic exposure more than doubled the risk of developing early-persistent asthma (odds ratio 2.3) [5]. The pattern is clear: more antibiotics, higher risk.
Where the evidence falls apart: eczema and ADHD
For other conditions like eczema and ADHD, the initial scary numbers largely disappear when you look closer. A nationwide Swedish study of over 720,000 children initially found that infant antibiotics raised eczema risk by 52% [3]. But when they compared siblings within the same family—which controls for shared genetics and parenting—the risk dropped to 24%, suggesting most of the original link was due to family factors, not the antibiotics themselves [3]. An Italian study of 73,000 children found no association at all between early antibiotics and eczema after accounting for 'protopathic bias' (the possibility that early eczema symptoms led to the antibiotic prescription, not the other way around) [8].
The story is similar for neurodevelopmental conditions. A meta-analysis pooling data from multiple studies found that early antibiotic use was associated with a 13% higher risk of autism and an 18% higher risk of ADHD [6]. However, when the analysis was restricted to sibling-matched studies—the gold standard for controlling for family genetics and environment—both associations vanished completely (odds ratios of 1.04 and 0.98, both statistically non-significant) [6]. This strongly suggests that the apparent link is due to shared family factors, not a direct effect of the antibiotics.
The pregnancy picture: specific risks and real reassurances
When it comes to antibiotics during pregnancy, the evidence is more nuanced. A large 2025 study of over 71,000 pregnancies found that the antibiotic trimethoprim-sulfamethoxazole (TMP-SMX) taken in the first trimester was linked to a 35% higher risk of any birth defect and a more than doubled risk of severe heart defects, compared to safer alternatives like penicillins [1]. This is strong enough evidence that doctors already avoid TMP-SMX in early pregnancy when possible. Importantly, the same study found that nitrofurantoin, another common UTI antibiotic, did not show a significantly elevated risk [1].
For other outcomes, the pregnancy evidence is more reassuring. A UK study of over 3,000 mother-child pairs found no link between maternal antibiotic use during pregnancy and infant eczema [7]. Similarly, the large obesity study found no association with antibiotics given during pregnancy or at birth [2]. The risk appears to be concentrated in the child's own exposure during infancy, not the mother's use during pregnancy.
About These Sources
This answer is built on 9 peer-reviewed studies — published from 2021 to 2026, 3 from 2024 or later, 6 in Q1 journals, collectively cited 137 times — selected as the most relevant from 11 studies that passed quality screening, drawn from 41 papers retrieved from a database of over 500 million.
Sources used in this answer
First-Trimester Antibiotic Use for Urinary Tract Infection and Risk of Congenital Malformations
In a cohort of 71,604 pregnancies, first-trimester exposure to trimethoprim-sulfamethoxazole was associated with a 35% higher risk of any congenital malformation and a more than doubled risk of severe cardiac malformations compared to β-lactam antibiotics; nitrofurantoin showed no elevated risk.
Early-life antibiotic exposure and the risk of overweight and obesity in children
In a cohort of 33,095 children, antibiotic exposure during the first 24 months of life was associated with a 20% higher risk of obesity (adjusted hazard ratio 1.20) and a 9% higher risk of overweight; no association was found for exposure before or at birth.
Association of Early Life Exposure to Antibiotics With Risk of Atopic Dermatitis in Sweden
In a nationwide Swedish cohort of 722,767 children, infant antibiotic exposure was associated with a 52% higher risk of atopic dermatitis, but this dropped to 24% in sibling-control analysis, indicating partial confounding by shared familial factors.
Early-Life Exposure to Antibiotics and Risk for Crohn’s Disease: A Nationwide Danish Birth Cohort Study
In a Danish cohort of 979,039 children, antibiotic use in the first year of life was associated with a 40% higher risk of Crohn's disease (adjusted hazard ratio 1.4), with a 4-fold higher risk for six or more courses; absolute risk remained very low (0.16‰ by age 11).
Early-Life Antibiotic Exposure and Childhood Asthma Trajectories: A National Population-Based Birth Cohort
In an Australian cohort of 4,318 children, any early-life antibiotic exposure (0-24 months) was associated with a 2.3-fold increased risk of early-persistent childhood asthma; second-generation cephalosporins showed a 2.7-fold increase.
Early Life Antibiotic Exposure and the Subsequent Risk of Autism Spectrum Disorder and Attention Deficit Hyperactivity Disorder: A Systematic Review and Meta-Analysis
In a meta-analysis, early-life antibiotic exposure was associated with a 13% higher odds of autism and 18% higher odds of ADHD, but these associations disappeared in sibling-matched analyses (odds ratios 1.04 and 0.98, non-significant), suggesting confounding by familial factors.
Early life exposure to antibiotics and laxatives in relation to infantile atopic eczema
In a UK cohort of 3,158 mother-child pairs, maternal antibiotic use in pregnancy was not associated with infantile atopic eczema, but infant antibiotic use in the first year was associated with a 59% increased risk of eczema at 12 months (adjusted odds ratio 1.59).
Early-life exposure to antibiotics and subsequent development of atopic dermatitis
In an Italian cohort of 73,816 children, early antibiotic exposure was not associated with atopic dermatitis after accounting for protopathic bias (hazard ratio 1.02, non-significant), suggesting earlier positive associations may be due to reverse causation.
Systematic Review: The Persistent Association Between Infant Antibiotic Exposure and Childhood Asthma After Accounting for Confounding by Indication and Reverse Causation
In a systematic review, the association between infant antibiotic exposure and childhood asthma persisted after accounting for confounding by indication and reverse causation, with a pooled odds ratio of 1.19 (95% CI 1.11-1.28), but sibling-matched analyses suggested residual confounding by respiratory illness severity.