Although a loss of heterozygosity (LOH) is commonly observed using microsatellite markers in a cell-proliferating malignant disorder, controversial findings of psoriasis, a keratinocyte-outgrowth disease, remain to be explained. It was hypothesized that unstable natures of the microsatellite markers for the polymerase chain reaction (PCR) might give a rise to either a false-positive or -negative LOH. Twentyone frozen skin tissues and 33 formalin-fixed paraffin-embedded archives were obtained from patients with psoriatic plaques and colorectal cancers, respectively. In the frozen psoriatic skin, two of the 17 microsatellite markers selected from 11 chromosomal arms were associated with artifact LOHs that were not reproduced in repeated PCRs. The remaining 15 stable microsatellite markers with few PCR artifacts demonstrated a borderline-level LOH in cases with an ambiguous heterozygosity such as a juxtaposed allelic band. Infrequent LOHs (3 out of 242 heterozygous markers, 1.2%) were detected in psoriatic cases with two separate alleles. In colorectal cancers, a set of the 15 stable microsatellite markers identified a minimal borderline-level LOH at the cut-off point that was same with that of psoriasis. These results indicate that the selection of reproducible microsatellite sequences and the cautious criteria for informative heterozygosity are required to obtain the reliable LOH results from variable genomic DNAs, and that psoriatic lesions harbor few LOH.