To assess the association between biomarkers of inflammation, cartilage and bone turnover with gender, Bath Ankylosing Spondylitis Disease Activity Index (BASDAI), Spondylitis Disease Activity Score (ASDAS) and bone marrow oedema in resonance magnetic imaging (MRI) of sacroiliac joints (SIJs) and radiological damage in early spondyloarthritis (SpA). Cross-sectional study of 60 patients (56.7 % females; mean age, 32.4 years) with early SpA. Sociodemographic data, clinical features, serum matrix metalloproteinase 3 (MMP-3), high sensitivity C-reactive protein (hsCRP), C-terminal cross-linking telopeptides of type I collagen (CTX-I) and urinary deoxypyridinoline, ASDAS, BASDAI, BASFI, BASRI and MRI of the SIJs were collected. The mean (SD) disease duration was 12.4 (6.8 months). Twenty-two (68.7 %) of the 32 patients had active sacroiliitis by MRI. MMP-3 and CTX I correlated with swollen joint (r = 0.515, r = 0.386, p = 0.01). hsCRP correlated with ESR (r = 0.303, p = 0.05), with CRP (r = 0.455, p = 0.01) and with total BASRI (r = 0.95, p = 0.05). Biomarkers were unrelated with the rest of variables. Levels of MMP-3 (44.3 ± 52.4 vs 24.7 ± 33.4, p < 0.05) and CTX-I (0.53 ± 0.45 vs 0.24 ± 0.38; p < 0.05) were higher in men. Our study shows that CTX-I and MMP-3 are a marker of peripheral disease activity in early SpA. Male gender had higher levels of CTX-I and MMP-3, which may indicate higher disease activity. Higher hsCRP levels trended towards correlation with more baseline radiographic damage. Therefore, these biomarkers may help identify a subgroup of patients who will need closer monitoring and more intensive treatment.