I personally have low HDL cholesterol: before I went on accutane at age 19 it was 32. Accutane dropped it down a bit too.

My question is does anyone know why HDL Cholesterol would be low?

This study and many others show the same thing: http://www.ncbi.nlm.nih.gov/pubmed/22447309

There's a free PDF for this paper on researchgate.net

This study didn't measure the subjects' diets, disclose whether they were on Accutane, or had any other diseases or medications that would confound results, so we can't draw any solid conclusions from it.

I'd imagine lower HDL cholesterol would be lower if those on Accutane were eating lots, or higher-than-average of the unhealthy fats to increase the drug's bioavailability.

The key is the insulin resistance mentioned in the study. You go through a period of insulin resistance in puberty. It's part of utilizing resources for growth & hormonal changes. I wasn't aware that we also had elevated HDL even though insulin is involved in HDL regulation & diabetes leads to cardiovascular disease & all kinds of decrepitude, but then, they didn't tend to test young people for things that we shouldn't have to worry about until retirement age.

You should be avoiding all high glycemic impacting meals, drinks & snacks. & might even need to go low GL.