Your First 90 Days After Diagnosis

The first 90 days after an inflammatory bowel disease diagnosis often feel crowded with tests, decisions, and new faces. This period usually focuses on understanding how severe the disease is, starting treatment, checking vaccines, and assembling a care team. A clear roadmap can make this early phase more manageable and set up better, safer control of inflammation over time.

Key Takeaways

• Early visits focus on confirming diagnosis, measuring disease extent, and getting baseline blood and stool tests. (guidelinecentral.com)

• Clinicians usually review vaccine history and infection risks before starting strong immune‑suppressing medicines. (academic.oup.com)

• Treatment choices in the first months depend on disease type, severity, and personal goals and preferences. (journals.lww.com)

• Building a team that includes gastroenterology, primary care, nutrition, and mental health support often improves long‑term care. (mdcalc.com)

• Regular follow‑up, symptom tracking, and planned labs help check whether early treatment is working as intended. (guidelinecentral.com)

The Big Picture in the First 90 Days

In the first months after diagnosis, most plans have three main goals. The care team wants to confirm how far inflammatory bowel disease (IBD) has spread, calm active inflammation, and lower future risks.

This usually means several appointments in a short time. Many people meet more than one clinician and may see new tests and medicines for the first time. It is normal for this period to feel intense, even if symptoms begin to improve.

Baseline Tests and Labs

Baseline testing gives a starting snapshot of health. Later results can be compared with this baseline to see whether treatment is working and whether any safety issues appear. (guidelinecentral.com)

Blood tests

Common early blood work may include:

• A complete blood count to look for anemia or signs of inflammation

• A chemistry panel to check kidney and liver function

• Inflammatory markers such as C‑reactive protein (CRP) or erythrocyte sedimentation rate (ESR)

• Nutrition‑related tests, such as iron studies, vitamin B12, folate, and vitamin D

These results help identify problems like anemia, low protein levels, or vitamin shortages that may need treatment alongside gut‑directed therapy.

Stool tests

Stool tests often serve two roles. First, they check for infections such as C. difficile or other gut germs that can mimic or worsen IBD. Second, tests like fecal calprotectin help estimate how much inflammation is present in the intestines. (guidelinecentral.com)

Stool tests may be repeated during the first year to see how inflammation responds to treatment, especially when symptoms change.

Imaging and endoscopy

Most people receive a colonoscopy with biopsies as part of diagnosis. Early after diagnosis, the care team reviews these findings in detail, including which parts of the bowel are affected and how severely.

Some people, especially those with Crohn’s disease, may also need imaging such as magnetic resonance enterography (MRE) or CT enterography to look at the small intestine. Imaging can reveal strictures, fistulas, or other complications that influence treatment choices.

Snapshot: Common baseline evaluations

Vaccines and Infection Screening

Because some IBD medicines lower the body’s ability to fight infection, preventive care usually starts very early. Guidelines recommend checking vaccine history near the time of diagnosis and updating routine non‑live vaccines when possible. (academic.oup.com)

Common topics in the first 90 days include:

• Annual inactivated flu vaccine

• COVID‑19 vaccination according to national schedules

• Pneumococcal vaccines for lung and bloodstream infection risk

• Hepatitis B vaccination for those not already immune

• Human papillomavirus (HPV) vaccine within the recommended age range

• Shingles vaccination for adults in eligible age groups

Live vaccines such as measles‑mumps‑rubella or varicella are usually given only when immune suppression is not yet in place and when allowed by national guidance. Screening for infections like tuberculosis and hepatitis B or C often happens before starting biologics or other strong immune‑modifying medicines. (academic.oup.com)

Choosing a Treatment Plan

In the first 90 days, the care team usually decides how aggressively to treat inflammation. Decisions depend on whether the person has Crohn’s disease or ulcerative colitis, how severe symptoms are, which parts of the bowel are involved, and whether complications are present. (journals.lww.com)

Treatment categories that may be discussed include:

• Aminosalicylates (5‑ASA) for mild to moderate ulcerative colitis

• Corticosteroids for short‑term control during flares

• Immunomodulators such as thiopurines or methotrexate in selected cases

• Biologic therapies that target specific immune pathways

• Small‑molecule drugs such as Janus kinase (JAK) inhibitors or S1P modulators

Many teams now follow a “treat‑to‑target” strategy. This means aiming not only for symptom relief but also for objective improvement in blood, stool, and scope findings over time.

Key questions often covered in early treatment visits include:

• How quickly should symptoms improve with the chosen plan?

• What side effects and safety monitoring are expected?

• How pregnancy plans, smoking status, or other conditions might affect options

• Preferences about infusions, injections, or pills

Building a Strong Care Team

IBD care usually involves more than one specialist. The first 90 days are a good time for clinicians and patients to clarify who does what.

Clarifying how to reach the team, how quickly they usually respond, and which symptoms count as urgent is an important part of this phase.

Monitoring Progress and Follow-up

The first months after diagnosis usually include several follow‑up visits. These visits check whether the chosen treatment is reducing symptoms and improving markers of inflammation.

Monitoring may involve:

• Symptom diaries or digital trackers to record pain, stool frequency, and urgency

• Repeat blood tests to watch inflammation and medicine safety

• Repeat stool tests such as fecal calprotectin when symptoms change

• Occasional imaging or endoscopy, especially if symptoms stay active

Guidelines also support screening for issues like low bone density, skin cancer risk, and mood disorders as part of broader preventive care. (mdcalc.com)

Emotional and Practical Adjustments

A new IBD diagnosis often brings fear, frustration, or grief. Many people also worry about work, school, relationships, or future plans.

Mental health screening and early support are recommended parts of IBD care, not optional extras. (mdcalc.com)
Support can include counseling, peer groups, online communities, and help with practical matters such as workplace or school accommodations.

FAQs

How many tests are normal in the first 90 days?

It is common to have several blood tests, at least one stool test, and at least one scope or imaging study in this period. The exact mix depends on disease type, severity, and which tests were already done before diagnosis.

Is it safe to get vaccines soon after diagnosis?

Most inactivated (non‑live) vaccines are considered safe in people with IBD, including those on many immune‑modifying medicines. Timing and specific choices should follow national immunization schedules and be coordinated between gastroenterology and primary care teams.

When might repeat colonoscopy be needed after diagnosis?

Some people have repeat colonoscopy within the first few years to assess healing or monitor higher cancer risk, while others wait longer. The timing depends on disease extent, severity, and response to treatment, and is usually decided together with the gastroenterology team.