Your First 90 Days After Diagnosis

A new diagnosis of inflammatory bowel disease can feel overwhelming. The first three months are about setting a solid foundation. This includes confirming the diagnosis and disease extent, getting baseline labs, updating vaccines before any immune‑suppressing medicines, choosing a treatment plan, and building a care team. A clear plan early on helps prevent complications and supports long‑term remission.

Key takeaways

• Confirm the diagnosis and disease extent, then get baseline blood, stool, and imaging tests to measure inflammation. (academic.oup.com)

• Review and update vaccines early, especially before starting immune‑suppressing therapy. (guidelinecentral.com)

• Screen for hepatitis B and tuberculosis before most advanced therapies. (journals.lww.com)

• Pick a treatment for induction and a plan for maintenance, and agree on how progress will be monitored. (guidelinecentral.com)

• Build a team that includes gastroenterology, primary care, pharmacy, nutrition, mental health, and surgery if needed. (journals.lww.com)

Weeks 1–2: Confirm the baseline

• Revisit the diagnostic workup. Most people need colonoscopy or flexible sigmoidoscopy with biopsies, plus small‑bowel imaging for Crohn’s disease. This defines where the disease is and how severe it is. (academic.oup.com)

• Baseline labs commonly include complete blood count, metabolic panel, C‑reactive protein, and iron studies, with stool fecal calprotectin to quantify gut inflammation. These help track changes over time. (gastro.org)

• If symptoms are new, stool tests may be used to rule out infections that can mimic a flare. Imaging or intestinal ultrasound may be added based on symptoms and location. (academic.oup.com)

Weeks 1–4: Vaccines and infection screening

Update vaccines as soon as possible, ideally before starting steroids, biologics, JAK inhibitors, or thiopurines.

• Core adult vaccines: influenza every season, Tdap as due, hepatitis B for all adults 19–59 and older adults based on risks, human papillomavirus through age 26 and up to 45 by shared decision making. Live vaccines are generally avoided during significant immunosuppression. (cdc.gov)

• Pneumococcal: adults with IBD who qualify because of immunosuppression can receive one dose of PCV20, or PCV15 followed by PPSV23 at the recommended interval. (cdc.gov)

• Zoster: recombinant zoster vaccine is recommended for adults 50 and older, and for immunocompromised adults starting at age 19. (cdc.gov)

• RSV: one‑time RSV vaccine for all adults 75 and older, and for adults 50–74 at increased risk of severe RSV. (cdc.gov)

• COVID‑19: people who are moderately or severely immunocompromised may need additional 2024–2025 vaccine doses; stay up to date per CDC. (cdc.gov)

Screen for infections that matter before immune‑suppressing therapy:

• Hepatitis B serology panel (HBsAg, anti‑HBc, anti‑HBs). Vaccinate if non‑immune and consider antiviral prophylaxis if surface antigen positive. (journals.lww.com)

• Latent tuberculosis with IGRA or TST plus chest imaging when indicated. Treat latent infection before starting most biologics or JAK inhibitors. (academic.oup.com)

• Check varicella immunity if uncertain, and complete needed vaccines before therapy when possible. (guidelinecentral.com)

Weeks 2–6: Choose and start treatment

Agree on an induction plan to calm inflammation and a maintenance plan to keep remission.

Discuss how quickly each option tends to work, how it is given, and safety monitoring. The plan should match disease severity, location, and personal preferences. (guidelinecentral.com)

Weeks 4–12: Monitor and adjust

• Noninvasive markers like fecal calprotectin and C‑reactive protein help confirm improvement and guide next steps, rather than relying on symptoms alone. Targets often use fecal calprotectin below about 150 µg/g along with a normal CRP. (gastro.org)

• Therapeutic drug monitoring is useful if response to an anti‑TNF drops, helping decide on dose adjustment or a switch. (gastro.org)

• Before thiopurines, check TPMT and consider NUDT15. Abnormal results call for dose reduction or choosing another therapy to avoid severe low blood counts. (cpicpgx.org)

Build the care team and plan

A strong team improves outcomes:

• Gastroenterologist to lead diagnosis, treatment choices, scopes, and monitoring.

• Primary care to coordinate vaccines, cancer screening, and chronic disease care.

• Pharmacist and IBD nurse for medication teaching and side effect checks.

• Registered dietitian for nutrition and deficiency recovery.

• Mental health professional for anxiety, depression, or stress management.

• Colorectal surgeon available for complications or when surgery is the best option. (journals.lww.com)

Agree on how to communicate, how to use the patient portal, and when to check labs or stool tests.

Health maintenance that starts now

• Skin protection and periodic skin checks, especially with thiopurines.

• Cervical cancer screening per guidelines, with annual screening if on immunosuppression.

• Bone health assessment when risk factors are present, and vitamin D and calcium as advised. (mdcalc.com)

• Colon cancer surveillance: for extensive ulcerative colitis or Crohn’s colitis, plan the first surveillance colonoscopy about 8 years after symptom onset, sooner and more often if primary sclerosing cholangitis is present. (guidelinecentral.com)

When to seek urgent care

Seek prompt care for fever above 101°F, severe belly pain, repeated vomiting, signs of dehydration, heavy rectal bleeding, jaundice, or sudden severe medication side effects.

What the next 90 days set up

By the end of three months, most people will have a clear diagnosis and extent, updated vaccines, a chosen induction and maintenance plan, and a monitoring schedule. The care team should be in place, with agreed check‑ins and a plan for flares and routine preventive care. This foundation supports safer treatment and better long‑term control. (journals.lww.com)