The predisposition of patients with lobular carcinoma in situ (LCIS) to develop invasive breast cancer (IBC) is well known. However, relatively little is known about the biologic characteristics, which may be involved in the development and progression of LCIS. This study evaluated 59 cases of LCIS (29 pure, 30 with synchronous IBC) for five biomarkers known to be important in IBC (ER, PgR, c-erbB-2, p53 and Ki-67 proliferation rate) by immunohistochemistry. A comprehensive analysis of loss-of-heterozygosity (LOH) was performed in 12 cases (10 pure, 2 with synchronous IBC) at 15 genetic loci on 9 chromosomes. LCIS demonstrated a low grade/favorable biophenotype that was not significantly different in cases with and without synchronous IBC (ER 98%, PgR 84%, c-erbB-24%, p53 19% and proliferation rate 2%). LOH was present in 80% of pure LCIS and the highest rates of LOH were at loci on 9p (30%), 16q (63%), 17p (33%) and 17q (50%). The clustering of LOH at these four foci suggests that inactivated tumor suppressor genes in these regions may be particularly important. LOH was present in both cases of LCIS with synchronous IBC and the LOH phenotype was shared by LCIS and IBC. Our findings suggest that five known prognostic factors in IBC do not have prognostic utility in LCIS. Multiple genetic mechanisms may be involved in the development of LCIS.