Rat apoA-I polymorphism has been analyzed in lymph and plasma. Two major proteins were present and their relative distribution was different in lymph and plasma lipoproteins. The basic protein (pI 5.60) was quantitatively most abundant among plasma lipoproteins and the acidic protein (pI 5.50) was predominant in lymph chylomicrons and lipoproteins. Microsequence amino acid analysis of the two proteins isolated by preparative isoelectrofocusing revealed that pI 5.50 apoA-I was proapoA-I with six additional amino acids (H2N-Ser-Glu-Phe-Trp-Gln-Gln) at the N-terminal end of "mature" apoA-I (pI 5.60 apoA-I). When radioiodinated proapoA-I was injected in rats, a conversion to "mature" apoA-I was observed and the process reached 92% completion in six hours. These data demonstrate the origin of apoA-I polymorphism in vivo.