The aim of this study is to clarify the association between serum leptin levels and the presence of syndesmophytes in male patients with ankylosing spondylitis (AS). Seventy-two male patients with AS and 20 age-matched healthy male controls were included. Patients were stratified by the presence of syndesmophytes. Serum leptin levels were measured and adjusted for body mass index (BMI). In addition, bone-specific alkaline phosphatase (BALP), osteocalcin, and telopeptide of type I collagen were determined. Patients with syndesmophytes were associated with older age (p < 0.001), longer disease duration (p = 0.003), and higher BMI (p = 0.038). Serum leptin levels and leptin per BMI (leptin/BMI) ratio were not different between AS patients and healthy controls. However, serum leptin/BMI ratio was significantly higher in patients with syndesmophytes compared to those without (p = 0.010). In multivariate analysis, higher serum leptin/BMI ratio remained significantly associated with the presence of syndesmophytes (p = 0.029). Moreover, serum leptin/BMI ratio was positively correlated with serum BALP (γ = 0.279, p = 0.039). However, there was no significant association between serum leptin/BMI ratio and bone mineral density. Serum leptin levels are elevated in male AS patients with syndesmophytes and were found to be correlated with bone formation marker, suggesting a potential role of leptin in new bone formation in AS.