Squamous/squamo-columnar junction dysplasia is generally divided into two tiers designated as low- and high-grade squamous intraepithelial lesions (L- and HSILs). This concept has been embraced for use at a number of different anatomical sites, including the vulva and anus. LSIL was previously thought to represent a step in a dysplastic progression, leading to HSIL and, ultimately, squamous cell carcinoma. While this may still be true in a small subset of LSILs, LSIL likely represents a rather heterogeneous group of lesions, with most LSILs having little malignant potential. This behaviour is true, despite a large proportion of LSILs also being infected with high-risk human papillomavirus (HPV). Some advocate for the use of the term "HSIL outcome" (vs. progression).

Cytologically, the cells show increased nuclear-to-cytoplasmic (N:C) ratio, but the amount of cytoplasm should be relatively abundant (compared to HSIL). The size of the nuclei should be at least three-times that of an intermediate cell. In this specimen, the presence of koilocytes is helpful, seen with the characteristic peri-nuclear halos.

LSIL and HSIL can often co-exist, and repeat cytology is generally recommended for patients with LSIL.