To evaluate the character and significance of microsatellite deoxyribonucleic acid allelic imbalance in laryngeal squamous cell carcinogenesis.

We investigated the frequency of expression and clinical relationships of loss of heterozygosity and microsatellite instability in 49 laryngeal premalignant and malignant lesions. Allelic imbalance was analysed using six polymorphic markers (D3S1234, D9S171, D9S1748, D9S162, D9SINFA and D17S796), via polymerase chain reaction – single sequence length polymorphism – silver staining.

Allelic loss was seen in 3.7 per cent of the six markers in hyperplastic lesions, 10.81 per cent in mild dysplasia, 26.03 per cent in moderate to severe dysplasia, and 38.67 per cent in laryngeal squamous cell carcinoma. Significant associations were found between allelic loss and clinical pathological grades (χ2 = 17.686, p = 0.000). No statistically significant difference was found in the frequency of microsatellite instability (χ2 = 0.314, p > 0.05). In the early stages of neoplastic change, the incidence of microsatellite instability was higher than that of loss of heterozygosity.

Allelic imbalance was associated with the carcinogenesis and progression of laryngeal squamous cell carcinoma. Microsatellite analysis might provide new approaches to early genetic detection for patients with premalignant laryngeal lesions.