This study investigates lipoprotein composition in diabetes before and after treatment with insulin or pioglitazone and its relationship to gene expression of five genes found in liver and intestine which are involved in cholesterol homeostasis. Thirty zucker diabetic fatty fa/fa and 10 lean rats were examined. mRNA for 3-hydroxy3-methylglutaryl coenzyme A reductase (HMGCoA), microsomal triglyceride transfer protein (MTTP), Niemann Pick C1-like 1 (NPC1L1) and ATP binding cassette transporters (ABC) G5 and G8 was determined using real-time, reverse transcriptase (RT-PCR). Cholesterol, triglyceride, apo B48 and apo B100 were elevated in chylomicrons and very low density lipoproteins (VLDL) of untreated diabetic animals (p<0.02). For similar blood glucose pioglitazone was more effective than insulin in normalising the lipoproteins. In diabetic animals, HMGCoA reductase, MTTP and NPC1L1 mRNA were significantly elevated (p<0.02) and ABCG5 and ABCG8 were significantly reduced (p<0.02) in the liver. Pioglitazone significantly reduced hepatic MTTP and NPC1L1 mRNA (p<0.0001) and significantly increased ABCG5 and G8 mRNA (p<0.0001) as compared to insulin. In conclusion diabetes was associated with major changes in mRNA levels of proteins involved in the regulation of post-prandial lipoproteins. Pioglitazone and insulin have different effects on post-prandial lipoprotein metabolism in part due their effect on genes regulating cholesterol synthesis and lipoprotein assembly.