Head and neck squamous cell carcinoma, including laryngeal cancer, is considered to progress from dysplasia to invasive cancer through well-defined clinical and histological stages. Numerous genetic alterations have been described in laryngeal squamous cell carcinoma, but the molecular mechanisms contributing to initiation and progression of laryngeal cancer are still poorly understood. Genomic, transcriptomic and protein alterations in laryngeal cancer progression are key areas for the current research aimed at finding instruments for classification, prognostication and patient-tailored treatment. We present a review of the current literature and discuss the use of array-based technologies in revealing the molecular portrait of laryngeal cancer.