Low-molecular-weight heparin and ultra-low-molecular-weight heparin are widely used as anticoagulant and antithrombotic drugs. An atmospheric pressure dielectric-barrier discharge procedure was developed to depolymerize heparin to low-or ultra-low-molecular-weight fragments. Dielectric-barrier discharge treatment of heparin resulted in several well-separated and uniform fragments. The structural character of digested fragments below 3,000 Da was elucidated. Expected digestion products such as sulfated disaccharide, sulfated tetrasaccharide, and pentasaccharides with alternatingly-linked N-acetyl glucosamine and iduronic acid were detected. The anticoagulant potential of the digested heparin was tested. The results indicated that dielectric-barrier discharge treatment can produce various molecular weight (MW) heparin fragments and maintain anticoagulant potency.