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Health condition · Clinically reviewed

Congenital anomalies, from antenatal screening to lifelong specialist care.

Around 2 to 4 percent of UK babies are born with a structural or functional anomaly. Modern screening, fetal therapy and paediatric services mean far more children now thrive.

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Why trust this guide

  • 01

    Clinically reviewed

    Written by our editorial team and reviewed by a registered UK clinician before publication.

  • 02

    Sourced from guidance

    Checked against NICE, RCOG, RCPCH, BPSU and NHS Genomic Medicine Service standards you can see at the end.

  • 03

    Current for 2026

    Reflects the newborn blood spot expansion for CAH and SCID, plus current fetal therapy pathways in the UK.

Key facts

Congenital anomalies at a glance.

The essentials for parents and families, in plain English, on what these conditions are and how UK services are set up to help.

  • What it is

    A structural or functional abnormality present from birth, whether obvious at delivery or discovered later in life.

  • How common

    Around 2 to 4 percent of UK live births, roughly 14,000 babies a year, and a major driver of infant mortality and lifelong disability.

  • The main categories

    Structural, chromosomal, single-gene, metabolic, haematological and functional anomalies, with big overlap between groups.

  • Commonest structural

    Congenital heart defects affect around 1 percent of births and remain the largest single group by number.

  • What causes it

    A mix of genetic, teratogenic and multifactorial influences, with no identifiable cause in about half of cases.

  • What helps most

    Preconception folic acid, tight diabetes and epilepsy control, immunisation, avoiding teratogens and a good antenatal pathway.

Why this guide matters

A hub, not a single diagnosis.

Because congenital anomalies span so many organs and specialties, this page is a map: what the categories are, how they are found and where UK families go next.

  • Prevention starts before pregnancy

    Folic acid, immunisation, controlled diabetes and epilepsy and a careful medication review reduce risk more than anything else.

  • Screening picks up much, but not all

    Combined test, NIPT and the 20-week scan catch many anomalies, but some are only apparent after birth or later in childhood.

  • Care is a team effort for life

    Fetal medicine, neonatology, paediatric surgery, genetics and community teams work together, often for many years.

How the diagnosis is made

From first scan to a clear plan.

The steps a UK antenatal, neonatal and genetics team will normally follow, in order, so you know what to expect and why.

  1. 01

    Screening

    Combined test and NIPT

    First-trimester combined screening and non-invasive prenatal testing look at the commonest chromosomal conditions.

  2. 02

    Screening

    20-week anomaly scan

    The mid-pregnancy ultrasound checks the brain, spine, heart, abdomen, kidneys and limbs against a national protocol.

  3. 03

    Screening

    Fetal echo and MRI where needed

    Targeted fetal echocardiography and selective fetal MRI clarify complex cardiac and neurological findings.

  4. 04

    Confirming

    Invasive testing if suspected

    Chorionic villus sampling or amniocentesis with chromosomal microarray confirms suspected genetic conditions.

  5. 05

    Confirming

    Newborn examination and NIPE

    The newborn and infant physical examination screens the heart, hips, eyes and testes within 72 hours and at 6 to 8 weeks.

  6. 06

    Planning

    Blood spot and specialist review

    The 5-day heel prick, hearing screen and clinical dysmorphology assessment shape the next round of tests.

  7. 07

    Planning

    Genomic testing and MDT plan

    Whole exome or genome sequencing via the NHS Genomic Medicine Service, then a multidisciplinary plan with genetic counselling.

Typical timeline: antenatal screening at 12 and 20 weeks, newborn checks in the first days and weeks, and genomic results over the months that follow.

Categories

The main groups of congenital anomalies.

Structural, chromosomal, single-gene, metabolic and functional groups, with the commonest examples from each and links to specific guides.

  • Cardiac anomalies

    Congenital heart defects such as septal defects, coarctation and valve disease, often picked up on scan or newborn check.

  • Neural tube defects

    Spina bifida, anencephaly and encephalocele, strongly linked to folate status in early pregnancy.

  • Craniofacial anomalies

    Cleft lip and palate, microtia, craniosynostosis, Treacher Collins and Pierre Robin sequence.

  • Musculoskeletal anomalies

    Clubfoot, developmental dysplasia of the hip, chest wall deformity, limb reduction, polydactyly and syndactyly.

  • Urogenital and GI anomalies

    Hypospadias, cryptorchidism, bladder exstrophy, oesophageal atresia, gastroschisis and diaphragmatic hernia.

  • Chromosomal conditions

    Down, Patau, Edwards, Turner and Klinefelter syndromes, plus microdeletions such as 22q11.2 (DiGeorge).

  • Single-gene and metabolic

    Cystic fibrosis, sickle cell, thalassaemia, haemophilia, muscular dystrophies and inborn errors of metabolism.

  • Red flag - severe respiratory or feeding difficulty

    Any newborn with cyanosis, respiratory distress, poor feeding or altered tone needs urgent neonatal review.

Explore specific conditions

Linked guides on individual anomalies covered in this hub.

Management

How congenital anomalies are managed in the UK.

Prevention, antenatal counselling, fetal therapy where available, neonatal surgery and lifelong specialist support, coordinated by a multidisciplinary team.

  • Preconception care

    Folic acid 400 micrograms daily (5 mg if diabetic, BMI over 30, on antiepileptics or with a previous NTD) plus a full medication review before pregnancy.

  • Antenatal MDT counselling

    Shared decision-making with fetal medicine, genetics and paediatric surgery so families understand the diagnosis, options and delivery plan.

  • Fetal therapy

    Laser for twin-to-twin transfusion, valves for CPAM and lower urinary tract obstruction, tracheal balloon for diaphragmatic hernia and open fetal surgery for spina bifida in specialist UK centres.

  • Neonatal stabilisation

    Planned delivery at a specialist centre with immediate resuscitation, neonatal intensive care and ready access to paediatric surgical teams.

  • Surgical correction

    Staged paediatric surgery for cardiac, craniofacial, gastrointestinal, urogenital and musculoskeletal anomalies where anatomical repair is possible.

  • Medical and metabolic care

    Endocrine, metabolic and cardiac medication, enzyme replacement and disease-specific therapy for single-gene and inborn errors of metabolism.

  • Rehabilitation and support

    Physio, occupational therapy, speech and language, feeding support, assistive equipment and community paediatric follow-up.

  • Genetic counselling

    Cascade testing for relatives, reproductive counselling and preimplantation genetic testing where a familial variant is identified.

What this guide is based on

The sources behind every claim on this page.

UK national guidance, screening programmes and specialist society standards, current at the time of last review.

Key references

Guidelines and standards we relied on.

A quiet reminder

This guide is for information, not medical advice.

Your midwife, obstetrician, paediatrician or clinical geneticist knows the whole picture and can tell you which parts apply to your family. If in doubt, get seen.

  • NICE. Antenatal care (NG201) and Fetal alcohol spectrum disorder (QS204).

  • RCOG and BMFMS. Green-top guidance on fetal medicine and prenatal diagnosis.

  • RCPCH and BPSU. Surveillance of rare paediatric and congenital conditions.

  • Public Health England / UK NSC. Fetal Anomaly Screening Programme and Newborn Blood Spot Programme (2025 expansion).

  • NHS England. Genomic Medicine Service and National Test Directory for rare disease.

Red flags

When a newborn or baby needs urgent review.

Some features in pregnancy, at birth or in the first weeks of life should trigger the same-day involvement of a paediatric team.

  • Severe respiratory distress at birth

    Cyanosis, grunting or apnoea in a newborn can signal a duct-dependent heart lesion, diaphragmatic hernia or airway anomaly and needs immediate resuscitation.

  • Absent or weak femoral pulses

    A classic sign of coarctation of the aorta and a reason for urgent cardiology review before discharge.

  • Failure to pass meconium in 24 hours

    May reflect Hirschsprung disease, anorectal malformation or intestinal atresia and warrants urgent paediatric surgical assessment.

  • Bilious vomiting in a newborn

    Green vomit in a baby is a surgical emergency until proven otherwise and needs an urgent upper GI contrast study.

  • Prolonged jaundice past 14 days

    Conjugated hyperbilirubinaemia may indicate biliary atresia, where the Kasai procedure works best before 60 days of life.

  • Ambiguous or atypical genitalia

    Needs urgent joint endocrine and specialist review, with a hold on sex assignment until the diagnosis is clear.

  • Dysmorphic features and multiple anomalies

    A pattern of features raises the chance of a chromosomal or syndromic diagnosis and should trigger clinical genetics input.

  • Positive blood spot screen

    A screen-positive result on the heel prick needs prompt confirmatory testing and specialist metabolic or haematology follow-up.

  • Family history of a genetic condition

    A known familial variant, consanguinity or previous affected pregnancy warrants preconception and antenatal genetic counselling.

Living with it

A lifelong path, walked with the right team.

Four things that make the biggest difference over the years for families living with a congenital condition.

A quiet reminder

You do not have to hold the whole story yourself.

A specialist nurse, condition-specific charity and community paediatric team share the load with parents, siblings and, in time, the young person themselves.

  1. 01 Team

    Build the right team early

    A named paediatrician, specialist nurse and disease-specific charity make navigating appointments, letters and school plans much easier.

  2. 02 Records

    Keep one shared record

    A single folder or app with letters, imaging, medication list and school plan avoids repeating the story at every new appointment.

  3. 03 Family

    Ask about cascade testing

    Where a genetic diagnosis is confirmed, testing relatives can pick up others who benefit from screening or reproductive advice.

  4. 04 Transition

    Plan the move to adult services

    Structured transition from paediatric to adult teams in the mid to late teens prevents people falling out of specialist follow-up.

Frequently asked

Everything we get asked about congenital anomalies.

Quick answers on how common they are, what causes them, and how UK screening and specialist services work.

  • What is a congenital anomaly?

    A structural or functional abnormality present from birth. It can be obvious at delivery, spotted on antenatal scan or diagnosed later in childhood or even adult life, and it may be isolated or part of a wider syndrome.

  • How common are birth defects in the UK?

    Around 2 to 4 percent of live births are affected, which is roughly 14,000 babies each year. Congenital heart defects are the largest single group at about 1 percent of births.

  • What causes congenital anomalies?

    Around 40 percent are primarily genetic, some are teratogenic (from maternal illness, infection, medications, alcohol or folate deficiency), most are multifactorial, and in about half of cases no single cause is identified.

  • What antenatal screening is offered in the UK?

    The combined test and non-invasive prenatal testing look at chromosomal conditions, the 20-week scan checks structure, and fetal echocardiography, fetal MRI or invasive testing are added when a specific concern is raised.

  • What does the newborn blood spot test cover?

    The 5-day heel prick screens for sickle cell disease, cystic fibrosis, congenital hypothyroidism and a panel of inherited metabolic diseases. In 2025 the UK programme is expanding to include congenital adrenal hyperplasia and severe combined immunodeficiency.

  • How can families reduce the risk in future pregnancies?

    Take folic acid before conception, optimise diabetes and epilepsy control, review medications for teratogenic risk, be up to date with rubella and varicella immunisation, avoid alcohol and smoking, and ask for genetic counselling if there is a family history.

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