Fresh Houttuynia cordata THUNB. is a Chinese materia medica generally used in Chinese medicine therapy. It possesses the actions of clearing heat, eliminating toxins, reducing swelling, discharging pus and relieving stagnation. However, dry H. cordata has traditionally been used in clinical application instead of the fresh counterpart. In this paper, the chemical profiles of H. cordata were established using fingerprinting techniques. A modified GC-MS method was developed in the comparison of fingerprints among fresh and dry herbs of H. cordata. It was shown that the varieties, as well as relative levels of chemical components, in the fresh herb were more abundant than in the dry counterpart. Fingerprinting profiles were found to be consistent for fresh herbs acquired from various production areas, but the relative abundance of peaks were varied. Besides, the chemical components among different medicinal portions of fresh herbs were found to be inconsistent. The developed fingerprint can be successfully applied to distinguish between fresh and dry herbs, as well as determining differentiation among different medicinal portions.