Geographic origin may represent a variable capable of influencing health status. This study aims to investigate the presence of differences of disease severity in Italian patients with fibromyalgia from different macro-regions. This retrospective, cross-sectional study involved patients included in the Italian Fibromyalgia Registry. Three geographical macro-regions were identified, comprising patients from Northern Italy, Central Italy and Southern Italy. Clinical differences (evaluated through PolySymptomatic Distress Scale [PSD], revised Fibromyalgia Impact Questionnaire [FIQR] and modified Fibromyalgia Assessment Status [FASmod]) among the geographical macro-regions were studied using one-way analysis of variance (ANOVA) and the Scheffé's test. A total of 6095 patients (5719 females and 376 males) were included, with 1957 from Northern Italy, 2979 from Central Italy and 1159 from Southern Italy. All studied clinical indices showed a trend indicative of greater disease severity in Southern Italy, followed by Northern Italy and then Central Italy (mean values for PSD: 19.97 ± 6.20 in Northern Italy, 18.61 ± 7.12 in Central Italy, 23.01 ± 5.66 in Souther Italy). These differences were statistically significant for the overall scores of all studied indices, evaluated with ANOVA (all p < 0.001) and in the head to head comparisons, evaluted with Scheffé's test. Geographic background is significantly associated with variations in the severity of fibromyalgia in Italian patients. This is the first study to demonstrate geographical origin-dependent intra-national differences in the severity of fibromyalgia. The results confirm the necessity of considering fibromyalgia within the context of the biopsychosocial model and of implementing healthcare policies targeted towards the most underserved regions.