The existence of a new, efficient algorithm for secondary structure prediction enables us to study the folding pattern of a messenger RNA chain. Our results indicate that successively longer RNA sequences with the same 5′-ends fold sequentially, usually keeping the stable close-range hairpin loops and rearranging the long-range stems. This path will shorten the time the messenger RNA molecule needs in order to attain its preferred structure. It can also align splicing sites in a favorable orientation before the whole molecule is synthesized. Our studies were carried out on the simian virus 40 late precursor and processed mRNA.