PegIntron is interferon alpha-2b, which is a "natural" interferon that is already present in the human body. It is produced by Schering-Plough in the United States and is a purely imported product. Pegasys is interferon alpha-2a, which is not a natural interferon. It is produced by the Swiss company Roche and is a domestically packaged product.

Both of these long-acting interferons use inactive polyethylene glycol to link the interferon , used to extend the half-life of the drug and achieve once-weekly administration. However, the size of the PEG molecule in PegIntron is 12KD, while the PEG molecule in Pegasys is 40KD, so the PEG molecule in Pegasys is 36KD larger than that in PegIntron.