This is a pilot study to compare levels of perceived injustice via the Injustice Experience Questionnaire in patients with fibromyalgia or rheumatoid arthritis. Two cohorts of patients, one with fibromyalgia (FM), one with rheumatoid arthritis (RA), completed the Injustice Experience Questionnaire, a visual analogue pain scale, and the Hospital Anxiety and Depression Scale (HADS). Inferential statistics were then used to determine whether participants in the two diagnostic groups had significantly different scores on the Perceived Injustice Questionnaire. This was done univariately using t tests and after adjusting for potential confounders using ANCOVA. We also examined crude associations between the variables using Pearson correlation coefficients, then examined the adjusted association between diagnostic group and perceived injustice using multivariable linear regression. Our final models were built in a blocked fashion by initially entering diagnostic category into the model, then entering other variables simultaneously using a stepwise strategy (p-to-enter ≤.05, p-to-remove ≥.10). A total of 126 participants (64 FM, 62 RA) completed all questionnaires. The FM group had a greater percentage of female participants, more severe pain, more severe anxiety and more severe depression. In unadjusted analysis, the FM group had higher Injustice Experience Questionnaire scores. When the RA and FM group scores for the Injustice Experience Questionnaire are adjusted for pain levels, there is no statistically significant difference between groups. Adjustment for HADS anxiety and HADS depression does not significantly affect the Injustice Experience Questionnaire scores after adjustment for pain. Fibromyalgia is associated with a higher level of perceived injustice than is seen with rheumatoid arthritis. This difference appears to be associated with higher levels of pain reported by fibromyalgia patients, and therefore may not be specific to the diagnosis. Prospective studies may help to resolve this issue.