Monoclonal antibody-based treatments for Crohn’s disease (CD) are thought to have the potential to alter disease course if used soon after diagnosis or before substantial mucosal damage occurs. However, identifying cohorts of newly diagnosed patients to examine the effects of early versus late use is challenging, as many patients do not see a health care provider who routinely prescribes biologic treatments as a first line therapy early in the disease course. We aimed to examine patterns of hospitalization and biologic use among newly diagnosed CD patients. A sample of 1,000 cases of CD was identified by at least two encounters associated with International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) code 555 in the U.S. military electronic health record from an eligible population of all active duty personnel diagnosed between 2001 and 2012. Individuals with ICD-9-CM 555 encounters within 1 year of enlistment were excluded because they may have had prevalent disease (n = 18). Inpatient encounters with an ICD-9-CM code 555 in the first 4 diagnosis positions were considered hospitalizations for CD. Outpatient Current Procedural Terminology (CPT) codes were used to identify the use of biologics (J0135-adalimumab, J0718-certolizumab, J1745-infliximab, J2323-natalizumab). Time to first use of a biologic was examined using a Cox proportional hazards model by year of CD diagnosis (prior to 2007, 2007–2012), adjusted for age, gender, race and hospitalization at diagnosis. Time to hospitalization by early biologic use within 6 months of diagnosis was also examined. The eligible 982 cases had a median age at diagnosis of 27 years (range 20–55 years) and median year of diagnosis of 2007. Median follow-up time after diagnosis was 2.0 years (range 0.02–11.6 years). Females comprised 17.6% of cases and 72.6% of cases were white. Hospitalizations occurred in 38.3% of patients with 48.2% of the hospitalizations occurring at the time of diagnosis. Multiple hospitalizations occurred in 16.6% of patients. Biologics were used by 9.4% (N = 92) of patients with 8.7% receiving infliximab and 0.9% (n = 9) adalimumab; no case received certolizumab, natalizumab, or both adalimumab and infliximab. First hospitalization preceded biologic use in 83.7% (n = 77) of biologic users and 20.7% (n = 19) received biologic only after at least 2 hospitalizations. First use of biologics occurred after 1 year of diagnosis in the majority of cases (median time to infliximab 1.9 years; range 8 days to 11.6 years). The time to first biologic did not differ by year of diagnosis (P = 0.2). The 7 early users of biologics were more likely to be hospitalized (excluding hospitalizations occurring within 7 days of diagnosis) subsequent to their use of biologics after adjustment for year of diagnosis, age, gender, race and hospitalization at diagnosis (HR 4.5; 95% CI, 2.1–9.9). Despite the availability of biologics and need for hospitalization in 2 out of 5 patients, early use of biologics was not common even in the recently diagnosed patients and those requiring hospitalization early in disease course. Among the small number of patients who used biologics soon after diagnosis, hospitalizations were more likely to occur.