Hyponatremia [p[Na]<136 mmol/L] is an independent risk factor for decreased bone mineral density (BMD). However, whether hyponatremia represents a surrogate marker, or a direct causal relationship to bone loss remains unknown. The aim of the study was to investigate the effect of salt replacement therapy on bone turnover markers (BTM) and BMD in patients with epilepsy and chronic hyponatremia. This prospective single-blinded randomized trial investigated serum BTM and BMD, evaluated by Dual Energy X-ray Absorptiometry (DXA), in 21 patients at baseline and following three months of salt replacement therapy. Patients with two consecutive measurements of hyponatremia prior to baseline and no known osteoporosis were included from the epilepsy out-patient clinic at Rigshospitalet, Denmark. Seven patients were randomized to placebo and 14 to salt intervention. The baseline p[Na] was 134 (130.5-140) mmol/L (median (IQR)). All patients had BTM within age-specific reference ranges at baseline. Following 3 months of intervention with 3-9 g of salt daily there was no difference in levels of procollagen type 1 N-terminal propeptide (P1NP) or C-terminal cross-linking telopeptide of type 1 collagen (CTX) between placebo and intervention. Nor was there any difference in BMD evaluated at the lumbar spine (L1-L4) or at the femoral neck or total hip. In our study, salt replacement did neither affect BTM nor BMD. However, due to the small size of the study, more studies are needed to further investigate this.