Background The aim of this study was to investigate subgroups of magnetic resonance imaging (MRI) findings for the spine and sacroiliac joints (SIJs) using latent class analysis (LCA), and to investigate whether these subgroups differ in their demographic and clinical characteristics. Methods The sample included 1037 patients aged 18-40 years with persistent low back pain (LBP). LCA was applied to MRI findings of the spine and SIJs. The resulting subgroups were tested for differences in self-reported demographic and clinical characteristics. Results A five-class model was identified: Subgroup 1, 'No or few findings' (n = 116); Subgroup 2, 'Mild spinal degeneration' (n = 540); Subgroup 3, 'Moderate to severe spinal degeneration' (n = 229); Subgroup 4, 'Moderate to severe spinal degeneration with mild SIJ findings' (n = 68); and Subgroup 5, 'Mild spinal degeneration with moderate to severe SIJ findings' (n = 84). The two SIJ subgroups (Subgroups 4 and 5) had a higher median activity limitation score (Roland Morris Disability Questionnaire calculated as a proportional score: 65 (IQR 48-78)/65 (48-78)) compared with Subgroups 1-3 (48 (35-74)/57 (39-74)/57 (39-74)), a higher prevalence of women (68 % (95 % CI 56-79)/68 % (58-78)) compared with Subgroups 2 and 3 (51 % (47-55)/40 % (33-46)), a higher prevalence of being overweight (67 % (95 % CI 55-79)/53 % (41-65)) compared with Subgroup 1 (36 % (26-46)) and a higher prevalence of previous LBP episodes (yes/no: 81 % (95 % CI 71-91)/79 % (70-89)) compared with Subgroup 1 (58 % (48-67)). Subgroup 5 was younger than Subgroup 4 (median age 29 years (IQR 25-33) versus 34 years (30-37)) and had a higher prevalence of HLA-B27 (40 % (95 % CI 29-50)) compared with the other subgroups (Subgroups 1-4: 12 % (6-18)/7 % (5-10)/6 % (3-9)/12 % (4-20)). Across the subgroups with predominantly spinal findings (Subgroups 1-3), median age, prevalence of men, being overweight and previous LBP episodes were statistically significantly lower in Subgroup 1, higher in Subgroup 2 and highest in Subgroup 3. Conclusions Five distinct subgroups of MRI findings in the spine and SIJs were identified. The results indicate that SIJ MRI findings not only can be seen as a part of the spondyloarthritis disease entity, but also are associated with age, gender and being overweight. Furthermore, the results indicate that LBP patients with SIJ MRI findings are more disabled compared with patients without SIJ MRI findings, and that moderate to severe spinal degeneration and/or SIJ MRI findings may be associated with recurrent pain.