The scaffold attachment factor A (SAF-A; Romig et al., 1992), a human nuclear protein which specifically binds vertebrate SAR (scaffold attached region) DNA, is identical with hnRNP-U (Kiledjian & Dreyfuss, 1992). In this paper, we report on the purification of two forms of this protein that can be chromatographically separated. We show that the purified proteins represent two isoforms, form 1 and form 2 hnRNP-U, which differ in their primary structure. Both isoforms bind to double- and single-stranded DNA and RNA. In addition, they form higher ordered nucleic acid/protein complexes and specifically bind and aggregate the human SAR element MII at physiological ionic strengths. Electron microscopic analysis shows that the isoforms differ from each other, as form 1 hnRNP-U aggregates into long unbranched filamentous protein/DNA complexes whereas form 2 hnRNP-U aggregates as spheres with an average diameter of 35 nm.