I know Pegasys is peginterferon alfa-2a & Pegintron is Peginterferon alfa-2b.
The "About" site says there is a slight difference in dosing. Not sure about side effect profile. There are a few links that compare the two & SVR on the bottom.
About web site:
The main difference between these two pegylated interferons is in the dosing.
Alfa-2a is used as a fixed weekly dose. Alfa-2b is used as a weekly dose based on the weight of the patient. There are other differences between the two drugs, but they are mostly technical and are used by the prescribing physician. For example, alfa-2a has a relatively constant absorption after injection and is distributed mostly in the blood and organs. But alfa-2b has a rapid absorption and a wider distribution in the body.
Until January 2008, no data directly compared these two medicines. That has changed with a large clinical study known as IDEAL. This should provide interesting results that will allow physicians additional insight into these powerful chronic hepatitis C therapies.
http://hepatitis.about.com/od/questions/f/alpha2a_2b.htm
_____________________
Here are some articles and links:
NE Journal of Medicine: Peginterferon Alfa-2b or Alfa-2a with Ribavirin for Treatment of Hepatitis C Infection
http://www.nejm.org/doi/full/10.1056/NEJMoa0808010
(the rates of sustained virologic response and tolerability did not differ significantly)
Peginterferon alpha-2a is associated with higher sustained virological response than peginterferon alfa-2b in chronic hepatitis C: systematic review of randomized trials
http://www.ncbi.nlm.nih.gov/pubmed/20187106
http://www.medhelp.org/posts/Hepatitis-C/Please-help-pegasys-pegintron-question/show/1647328
Peg-interferon alpha-2a versus Peg-interferon alpha-2b in nonresponders with HCV active chronic hepatitis: a pilot study.
(nonstatistically significant differences)
http://www.ncbi.nlm.nih.gov/pubmed/18778199