Two species of lipoproteins containing apoA-I (A-ILp), lipoprotein containing apoA-I and apoA-II (LpA-I/A-II), and lipoprotein containing apoA-I but no apoA-II were isolated from 12 girls with insulin-dependent diabetes mellitus (IDDM) and from 19 healthy controls using affinity chromatography. When characterizing the lipid and apolipoprotein compositions, we noted compositional changes. In A-ILp, the levels of lipid, except for triglyceride, and the level of apoC-III were significantly higher in IDDM. In LpA-I/A-II, the levels of lipids, except for triglyceride, the levels of apoC-III, and the ratio of apoA-I to apoA-II were significantly higher in IDDM. In lipoprotein containing apoA-I but no apoA-II, the levels of all lipids and apolipoproteins in IDDM were similar to those in the controls. The percent phospholipid in A-ILp and LpA-I/A-II was significantly higher in IDDM. All of these changes of A-ILp are similar to those associated with the reduced risk in the nondiabetic population. However, apolipoprotein changes of LpA-I/A-II may possibly be related to the accelerated atherosclerotic processes noted in patients with IDDM.