The purpose of this study was to investigate the application of salmon atelocollagen (SAC) to a scaffold. SAC has a low denaturation temperature and needs to be cross-linked before being used as a scaffold. In the present study, SAC was cross-linked by 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC) or dehydrothermal treatment (DHT). The material properties (degree of cross-linking and solubility in phosphate-buffered saline) of the SAC scaffolds cross-linked by EDC (EDC-SAC) and DHT (DHT-SAC) were evaluated. It was found that EDC-SAC had a high degree of cross-linking and high stability compared with DHT-SAC. Human periodontal ligament (HPDL) cells were cultured in the scaffolds for 2 weeks in vitro, and the activities (proliferation rate and alkaline phosphatase [ALP] activity) of HPDL cells cultured in EDC-SAC and DHT-SAC were compared with those cultured in bovine atelocollagen (BAC) scaffolds cross-linked by EDC (EDC-BAC) and DHT (DHT-BAC), respectively. The proliferation rate of HPDL cells cultured in EDC-SAC was equivalent to that in EDC-BAC, and the ALP activity in EDC-SAC was found to be significantly higher than that in EDC-BAC. In the cross-linking by DHT, the cell proliferation rate and the ALP activity in DHT-SAC were lower than those in DHT-BAC. DHT seemed to provide insufficient cross-linking, and DHT-SAC was found to be breakable and contractile, resulting in less cell activity. In contrast, there was no difference in the thermal stability, porous structure, and cell proliferation rate between EDC-SAC and EDC-BAC. In addition, the collagen helix of EDC-SAC was found to be partially denatured, and this structure resulted in the enhancement of ALP activity of HPDL cells compared with that using EDC-BAC. In conclusion, our results indicate that EDC-SAC could be used as a scaffold for in vitro culture.