We conducted a biodistribution study in HT-1080 bearing mice to investigate the drug targeting mechanism and the cause of side effects of the new dextran-peptide-methotrexate conjugates. HT-1080 is a human fibrosarcoma cell line that is known to overexpress matrix-metalloproteinases (MMPs). The experiments compared conjugates carrying MMP sensitive peptide linkers, conjugates carrying MMP insensitive linkers, and free methotrexate. Passive targeting was evidenced by the prolonged plasma circulation and higher tissue accumulations of both types of the conjugates compared to free methotrexate. Independent of the peptide sequence of the linker, the ratio of drug accumulation at the tumor versus drug accumulation at the major site of side effects (small intestine) for either conjugate was increased by the effect of enhance permeation and retention (EPR). The conjugate released a sufficient amount of peptidyl methotrexate to cause inhibition of tumor growth. There was no significant difference in drug accumulation at the tumor site between the MMP-sensitive and the MMP-insensitive conjugates. We concluded that the tumor targeting effect of the dextran-peptide-methotrexate conjugate was dominantly due to passive targeting and EPR. The difference in the systemic side effects observed for conjugates with different linkers could probably be attributed to their varying susceptibility towards enzymes in normal tissues. © 2006 Wiley-Liss, Inc. and the American Pharmacists Association.