SCP1, a major protein component of synaptonemal complexes (SCs), is probably a constituent of the transverse filaments (TFs). The protein consists of three domains: a short, proline-rich N-terminal part, a stretch of 700 amino acid residues capable of forming an amphipathic alpha-helix, and a C-terminal domain of 240 amino acid residues which is capable of binding to DNA. To analyze the orientation of SCP1 molecules within SCs, we elicited polyclonal antibodies against three non-overlapping fragments of SCP1, which comprise, respectively, the N-terminus, the C-terminus, and a fragment from the middle of the SCP1 molecule. Using these antibodies, we performed immunoelectron microscopy on SCs in two types of preparations, namely, surface-spread spermatocytes and ultrathin sections of Lowicryl-embedded testicular tissue of the rat. For each of the three antibodies used, the distribution of immunogold label on surface-spread spermatocytes differed significantly from the distribution of label on sections. Masking of SCP1 epitopes within the lateral elements (LEs) and the central element (CE) of SCs in surface-spread preparations and the influence of the surface morphology of the spreads on the labeling pattern were considered as possible explanations for these differences. We therefore relied on the results from sections for the localization of epitopes. On the basis of the distributions of immunogold label in Lowicryl sections and the predicted secondary structure and dimensions of SCP1 molecules, we present the following model: the C-terminus of SCP1 molecules lies in the inner half of the LE, the molecules protrude from the LE through the central region into the CE, and end up with their N-terminus between the center of the CE and the opposite LE, so that the N-termini of SCP1 molecules from opposite LEs overlap. The model has several implications for the assembly of SCs and the possible functions of SCP1.