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Saturated fat increases both "bad" LDL-cholesterol and "good" HDL-cholesterol. 
Background: In 2010 the USDA published it's last update on the dietary guidelines for Americans. Part D. Section 3 covered the science base for fatty acids and cholesterol (1). The report states that consumption of carbohydrates instead of saturated fat (SFA) will decrease levels of "bad" LDL-cholesterol:

Replacement of SFA with carbohydrates decreased plasma total and LDL cholesterol.

But how will this change in macronutrients influence levels of "good" HDL-cholesterol? Scientific research: In 2003, a group of Dutch researchers examined the effects on cholesterol of replacing carbohydrates with dietary fats. They searched the scientific literature for all controlled trials on this topic. A total of 60 trials were included in the final meta-analyses.
Results can be seen in the table below: Effects on serum cholesterol of replacing carbohydrates by saturated fats can be seen in the red rectangle. Both LDL- and HDL- cholesterol increased significantly (P = < 0.001). As a consequence, total cholesterol levels also rose. Noticeable, saturated fat increased HDL-cholesterol to a larger extend than monounsaturated fatty acids (MUFA) and polyunsaturated fatty acids (PUFA).
The ratio total:HDL-cholesterol did not change with increasing intakes of saturated fats.

1) US Department of Agriculture and US Department of Health and Human Services. Report of the Dietary Guidelines Advisory Committee on the dietary guidelines for Americans, 2010. http://www.cnpp.usda.gov/DGAs2010-DGACReport.htm
2) Mensink RP et al. Effects of dietary fatty acids and carbohydrates on the ratio of serum total to HDL cholesterol and on serum lipids and apolipoproteins: a meta-analysis of 60 controlled trials. Am J Clin Nutr. 2003 May;77(5):1146-55. http://www.ncbi.nlm.nih.gov/pubmed/12716665