Background: Pain is known to affect over 70% of individuals with inflammatory bowel disease (IBD), with abdominal and musculoskeletal (MSK) pain representing the most common complaints in this population. Although possible mediating and overlapping pathways have been proposed in the development of MSK pain in IBD, the multifactorial nature of painful conditions is not well understood nor fully captured. Aims: Primary aims are to characterize MSK pain in individuals with IBD through a national survey, in order to identify patient subgroups based on self-reported features of pain and assess how these subgroups differ with regards to demographics, comorbidity, and IBD characteristics. Methods: The present study is a cross-sectional online survey of adults with IBD and self-reported pain, living in New Zealand. The survey includes a range of measures examining demographics and comorbidity, IBD status (type, activity, and severity of IBD course), and pain status (intensity, location, interference, and quality). Latent class analysis will be used to generate mechanism-based subgroups of pain in this population Discussion: The present study will gather data on the multidimensional experience of self-reported MSK pain in IBD, and describe subgroups of pain in this population. Subgrouping has been shown to generate distinct profiles of patients with similar attributes, while permitting comparison of features between subgroups. Use of mechanism-based classification provides the opportunity to understand differing and potentially overlapping contributions of pathophysiological pain mechanisms. Results from the present study will be used to develop a clinical framework for assessing and describing MSK pain in IBD.