Abstract Background Early diagnostics of axial spondyloarthritis (axSpA) remains a challenge. Traditional imaging one-plane sacroiliac joint (SIJ) MRI assessment is used. By introducing a two-plane assessment system, the objective was to analyse the differences in SIJ MRI changes in early axSpA compared with changes in patients with mechanical back pain (MBP) by exploring the differences in volume and location. Methods MRIs in the early diagnostic state of 25 axSpA patients (mean age 31.3 years) and 59 MBP patients (mean age 32.3 years) were included. The MRIs were assessed by two readers regarding the distribution of bone marrow edema (BME) in 14 joint portions and structural changes in six joint portions in addition to SIJ anatomical variations and lumbar spine disc degeneration. Results AxSpA patients had a significantly higher overall BME sumscore (volume) of 25.1 compared to MBP patients 6.8, p < 0.005. The MBP group had the highest prevalence (66%) and sumscore (5.7) in the middle anterior sacrum. The axSpA group had significantly higher prevalence and sumscores in all joint portions except the three cartilaginous anterior sacral joint portions, including the ligamentous compartments (prevalence 40–60% compared to 8–15%, p both < 0.005). The axSpA group had also a significantly higher prevalence of erosions and fatty marrow disposition, but there were no differences in the prevalence of anatomical variations except the bipartite iliac bony plate. Conclusions AxSpA patients demonstrated a widespread distribution of both inflammatory and structural changes, including high BME occurrence in the ligamentous joint portions whereas patients with MBP had the highest occurrence of BME in the middle anterior sacrum. These findings may help differentiate axSpA patients from other back pain conditions in the early diagnostic phase.