Case-control studies have shown that Crohn’s disease (CD) patients have a different microbial composition than healthy individuals. Although the causes of CD are unknown, epidemiological studies suggest that diet is an important contributor to CD risk, potentially via modulation of bacterial composition and gut inflammation. We hypothesized that long-term dietary clusters are associated with gut microbiome compositions as well as gut inflammation. Our objectives were to identify dietary patterns and assess if they are associated with alterations in specific gut microbial compositions and subclinical levels of gut inflammation in a cohort of healthy first-degree relatives (FDRs) of CD patients.