First Trimester COVID-19 Shot Linked to Birth Defects in New Registry Study

A new registry-based cohort study out of Iran published in Sage Journals on June 15, 2026, has found a higher incidence of congenital anomalies, or birth defects, in babies born to women who received a COVID-19 shot within the first trimester of pregnancy compared with those who did not get vaccinated or were vaccinated after 12 weeks of pregnancy. The vaccinated women received COVID vaccines that did not use mRNA technology but were manufactured using inactivated whole-virus or viral-vector platforms, and the most common birth defects in their newborns affected the heart and palate.

Conducted by researchers at Yasuj and Hormozgan Universities of Medical Sciences in Iran, the study found that atrioventricular septal defects (AVSD) and cleft palate were more frequently observed among babies born to women vaccinated during the first trimester compared with unvaccinated women. The U.S. Centers for Disease Control and Prevention (CDC) define AVSD as a congenital heart defect that affects the valves and walls between the heart’s upper and lower chambers and note that the condition can cause lifelong complications. The CDC also notes the condition is common in babies with Down syndrome.^{1 2}

To conduct the study, researchers enrolled 1,352 pregnant women registered in Iran’s national electronic health record system, known as SIB, across two provinces during 2022 and 2023. Drawing from every eligible woman in the system during the study period, participants were divided into three groups: 303 unvaccinated women, 262 women vaccinated during the first trimester, and 787 women vaccinated after 12 weeks of gestation.¹

Birth defects were identified through routine prenatal ultrasound scans recorded in the SIB registry between 18 and 20 weeks of gestation and were not systematically confirmed after birth. Among women vaccinated during the first trimester, AVSD was observed in 2.3 percent of cases, compared with zero percent among unvaccinated women and 0.1 percent among women vaccinated after 12 weeks. Cleft palate was observed in 0.8 percent of first-trimester-vaccinated women, compared with zero percent in both other groups.¹

Researchers used descriptive statistics and standardized mean differences to compare anomaly rates across groups. The standardized mean difference for AVSD between the unvaccinated and first-trimester-vaccinated groups was 0.22, which the study’s own threshold classifies as a moderate effect size. Because individual birth defects identified in the study were rare, the number of events per group was too low to support multivariable regression, the standard method for controlling confounding factors.

The authors characterized their findings as preliminary and “hypothesis-generating” but not proof of a causal connection between the development of heart and cleft palate defects in the babies born to mothers who received the COVID shot during the first trimester.¹

Study Cohort Used Only Inactivated Whole-Virus or Viral-Vector Platforms Not Available in the U.S.

No mRNA COVID shots were administered to any study participant. All women in the cohort study were given COVID vaccines using an inactivated whole-virus plaform or viral-vector platform, neither of which is currently authorized in the U.S. In 2023, the FDA revoked the only U.S.-authorized viral-vector COVID vaccine, which was manufactured by Johnson & Johnson, following reports of a rare but serious blood clotting condition and “low consumer demand.” This left mRNA biological products developed by Pfizer/BioNTech and Moderna/NIAID as the sole COVID shots available in the U.S., even though the mRNA COVID shots carry risks of serious inflammatory heart conditions and manufacturers were eventually required by the FDA to update product labeling to communicate these risks.^{1 3 4}

Writing in his Focal Points Substack about the Iranian cohort study in pregnant women, epidemiologist Nicolas Hulscher, MPH, noted that if the mRNA COVID shots been included in the study, the findings “probably would have revealed even worse birth defect rates.” The Iranian study references earlier studies that relied on passive surveillance systems, which did include mRNA COVID shots and found “no increased risk compared with those unvaccinated in the first trimester.” However, the Iranian study authors note:

While these comparative studies [which included mRNA COVID shots] suggest that early pregnancy vaccination is not linked to a broad increase in major structural anomalies, our descriptive analysis found slightly higher frequencies of atrioventricular septal defects (AVSD) and cleft palate in women vaccinated inside the teratogenic window.

The teratogenic window is defined in the study as the period in which a woman “received at least one dose of COVID-19 shot from conception up to 11w and 6d.”^{1 5}

Study Authors Urge Research To Clarify Whether Vaccine-Induced Inflammatory Responses in Pregnant Women Affect Fetal Development

In their comments, the Iranian study authors pointed out that potential biological mechanisms linking maternal vaccination during pregnancy to fetal developmental and long-term neurodevelomental and neuropsychiatric outcomes in infants born to women vaccinated during pregnancy have not been fully investigated. They said, “further research, including experimental and animal studies, is needed to elucidate whether immune-mediated pathways may play any role in fetal development following vaccination.” They went on to state:

To date, there is no direct evidence demonstrating that maternal inflammatory responses induced by COVID-19 vaccination adversely affect fetal development or increase the risk of congenital anomalies. However, previous studies have shown that maternal immunization with inactivated influenza vaccines during pregnancy may be associated with transient increases in inflammatory biomarkers. This has led to broader interest in the concept of maternal immune activation and its potential implications for fetal and neonatal development. Evidence from animal models and selected human studies suggests that maternal immune activation during pregnancy may be associated with long-term neurodevelopmental or neuropsychiatric outcomes in offspring, possibly mediated by pro-inflammatory cytokines affecting placental function or fetal brain development.

Study Points to Mixed Messaging Around Vaccine Recommendations for Pregnant Women

The study authors acknowledge that “many countries commonly advise that women who are pregnant should be vaccinated against COVID-19 during their pregnancy.” This aligns with U.S. messaging, where the American College of Obstetricians and Gynecologists (ACOG) “strongly recommends” in its Conversation Guide for Clinicians that pregnant women receive a COVID-19 shot “in any trimester.”^{1 6}

They also acknowledge limitations around the size of the first-trimester exposure group due to “prevailing recommendations to delay vaccination until after the first trimester;” a marked divergence between Iranian and U.S. vaccination guidance. As the study authors state, “Although the overall sample size was relatively large, the number of fetuses exposed to COVID-19 vaccination during the critical teratogenic window was limited, primarily because vaccination during the first trimester was uncommon due to prevailing recommendations to delay vaccination until after 12 weeks of gestation.”

Because Iranian guidance discourages first-trimester vaccination, the group of women vaccinated in the first trimester was small. If the study had been conducted in the U.S., where ACOG recommends vaccination in any trimester, that group would have been considerably larger.^{1 6}

The ACOG Conversation Guide for Clinicians also states that “COVID-19 vaccines may be administered simultaneously with other vaccines, even though the safety of administering multiple vaccines simultaneously, including any synergistic effects, has not been established in clinical studies in pregnant or non-pregnant populations.^{1 6}

Hulscher noted the contrast between the study’s findings and U.S public health and medical trade organization guidance: “These findings arrive as major public health organizations—including the American College of Obstetricians and Gynecologists (ACOG), the Society for Maternal-Fetal Medicine (SMFM), the World Health Organization (WHO), and many national health agencies—continue to recommend COVID-19 vaccination during pregnancy.”⁵

CDC Officials Revise Vaccination Guidance for Pregnant Women as Reproductive Outcome Data Accumulates

In 2025, U.S. Secretary of Health and Human Services Robert F. Kennedy, Jr. called for a federal review of administering COVID shots during pregnancy, citing insufficient long-term reproductive safety data, prompting the CDC to revise its vaccination guidance for children and pregnant women.⁷

The Iranian study adds to a growing body of research linking COVID shots to adverse reproductive outcomes. Among recent findings, a June 2025 Israeli study found an association between administration of mRNA COVID shots during the first trimester of pregnancy and elevated rates of pregnancy loss. In a population-based Czech study published in the International Journal of Risk & Safety in Medicine, researchers reported lower rates of successful pregnancy among women who received a COVID shot prior to conception compared with those who did not, and European researchers documented birth rate declines across 19 countries following peak COVID shot uptake in late 2021.

Provisional data released by the CDC in April 2026 show that fertility rates in the United States have reached some of the lowest levels on record.^{1 3} “These organizations must be held accountable for their reckless actions that have resulted in grave harm to unborn children,” Hulscher wrote.⁵

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