The updated COVID vaccines have a safety profile consistent with earlier versions, meaning the side effects are mostly mild and short-lived. Across multiple federal surveillance systems tracking millions of doses, no new or unexpected safety concerns emerged during the 2023-2024 season, and the 2024-2025 formulas use the same platform with an updated viral target. Here’s what the monitoring data actually shows.
What Changed in the Updated Vaccine
The 2024-2025 COVID vaccines target a single strain called KP.2, a descendant of the Omicron lineage. The FDA initially directed manufacturers to target a strain called JN.1, then shifted to KP.2 as the virus continued evolving and cases rose. The underlying technology didn’t change. Pfizer and Moderna still use mRNA, while Novavax offers a protein-based option that works differently: it delivers a lab-made copy of the spike protein along with a plant-derived ingredient that helps activate your immune system.
Both the mRNA vaccines received full FDA approval for adults and emergency use authorization for younger age groups. Novavax operates under emergency use authorization. These aren’t experimental products at this point. The mRNA platform has been administered billions of times worldwide since 2021, and each seasonal update goes through the same regulatory review process.
Common Side Effects
The CDC’s V-safe surveillance system, which collects data directly from vaccinated people, found that reactions during the first week after the 2023-2024 dose were similar to the previous season. The most frequently reported side effects across all COVID vaccine types are soreness at the injection site, fatigue, headache, muscle aches, fever, and nausea. These typically resolve within a day or two.
If you’re planning to get your flu shot at the same visit, you may notice slightly more fatigue, headache, and muscle ache compared to getting the COVID vaccine alone. A CDC study found these reactions were mostly mild and cleared up quickly. There’s no recommended waiting period between the two vaccines, so getting both at once is considered safe and saves you a trip.
Rare but Serious Risks
The two serious risks that remain on the radar for mRNA COVID vaccines are myocarditis (inflammation of the heart muscle) and, to a lesser extent, a nerve condition called Guillain-Barré syndrome.
For myocarditis, the estimated rate based on health insurance claims data is about 8 cases per million doses in people ages 6 months through 64. The risk is highest in males ages 12 to 24, where it rises to roughly 27 cases per million doses. Most vaccine-related myocarditis cases are mild and resolve with rest, but it’s a real consideration, particularly for young men. This risk is included in the official warning labeling for both Pfizer and Moderna vaccines.
During the 2023-2024 season, the CDC’s Vaccine Safety Datalink flagged two statistical signals worth noting. One was a possible increase in Guillain-Barré syndrome after the Pfizer vaccine in adults 65 and older. If the signal reflects a true risk, the estimated excess would be about 4 cases per million doses, which is in line with rates seen with other vaccines for adults. The second signal involved ischemic stroke after mRNA vaccines in older adults, though the CDC stated this signal alone doesn’t provide enough evidence to confirm a safety concern and a follow-up study is underway.
No other new or unexpected safety issues were identified by any of the three major surveillance systems (VAERS, V-safe, or the Vaccine Safety Datalink) during that season.
The Protein-Based Alternative
If you prefer to avoid mRNA technology, the Novavax vaccine uses a more traditional approach. It contains a lab-grown version of the spike protein paired with an adjuvant derived from the bark of the soapbark tree. Post-authorization safety monitoring shows a similar profile to earlier Novavax formulations. The most common reports include headache, dizziness, fatigue, fever, chest pain, shortness of breath, and muscle pain. Anaphylaxis and myocarditis/pericarditis are listed as identified risks in the Novavax authorization documents as well, though no new safety signals have been identified for this vaccine.
Safety During Pregnancy
COVID vaccination during pregnancy has been studied in large populations, and the findings are reassuring. A meta-analysis covering more than 862,000 individuals found that infants born to vaccinated mothers were 15% less likely to be born prematurely and 20% less likely to need neonatal intensive care compared to infants of unvaccinated mothers. Vaccination during pregnancy also reduced COVID-related emergency department and urgent care visits by 52%, and a completed two-dose mRNA series was 61% effective at preventing hospitalization in infants under 6 months.
No association has been found between COVID vaccination and miscarriage, stillbirth, preterm birth, birth defects, preeclampsia, or gestational diabetes. Pregnant people don’t experience higher rates of side effects than anyone else, and vaccination has shown no measurable effect on fertility.
Vaccines for Children
Children ages 5 and older follow a straightforward schedule: a single updated dose, regardless of how many COVID vaccines they’ve had before. For previously unvaccinated children ages 6 months to 4 years, a multi-dose initial series is needed (three Pfizer doses or two Moderna doses) before the updated formula. Children who already completed that initial series need just one updated dose. The recommended waiting period between a previous COVID vaccine and the new dose is at least 8 weeks for most age groups.
How Safety Monitoring Works
COVID vaccines are tracked by overlapping surveillance systems that catch different types of problems. VAERS collects voluntary reports from anyone, which is useful for spotting unexpected patterns. V-safe actively surveys vaccinated people about their symptoms in the days following their shot. The Vaccine Safety Datalink pulls from medical records of millions of people in large healthcare systems, allowing researchers to compare rates of specific conditions in vaccinated versus unvaccinated populations. When a statistical signal appears in one system, it triggers deeper investigation in the others. This layered approach is why rare events like myocarditis were identified relatively quickly after the initial vaccine rollout and continue to be tracked with each updated formula.