The serum N-terminal telopeptide of type I collagen (NTx) is significantly higher in patients with Crohn disease (CD) than in healthy individuals and patients with ulcerative colitis. This study aimed to investigate whether an elevated serum NTx level is a risk predictor of osteoporosis in patients with CD. Based on whether the femoral Z-score decreased over a 2-year period, 41 CD patients were divided into the ΔZ-score <0 group (Z-score decreased) and the ΔZ-score ≥0 group (Z-score did not decrease). The risk predictors of a femoral Z-score decrease were examined. Furthermore, we investigated the correlations between the ΔZ-score (which represents the change in the Z-score over a 2-year period) and the mean levels of biomarkers, including the Crohn Disease Activity Index (CDAI), serum albumin, C-reactive protein, and bone metabolism markers (including NTx) measured initially (i.e., in our previous study) and 2 years later (present study). The relationships between anti-tumor necrosis factor α (anti-TNF-α) therapy and serum NTx levels were also examined. Although there was no correlation between the mean CDAI and the ΔZ-score, the mean serum NTx and albumin levels were significantly correlated with the ΔZ-score (P<0.01 and P = 0.02, respectively). Furthermore, the femoral Z-score tended to be lower in the anti-TNF-α administration group than in the non-administration group. These observations indicated that an elevated serum NTx could be a useful marker for predicting a decrease in the femoral bone mineral density in CD patients. Anti-TNF-α therapy maintained an elevated serum NTx level, suggesting that treatment with anti-TNF-α may help control increased bone resorption in CD patients.