Apoptotic cell death, in conjunction with mitosis, plays an important role in maintaining tissue homeostasis. Many cancer treatment modalities have been shown to induce apoptosis in sensitive cells. The purpose of this study was to determine the amount of apoptosis in-situ, the expression of apoptosis related genes p53 and bcl-2 and the proliferative marker nucleolar organiser region (AgNOR), in squamous cell carcinoma (SCC) of the larynx and correlate the results to clinical outcome. Paraffin-embedded samples of 66 patients with laryngeal SCC (34 glottic, 24 supraglottic and 8 transglottic) treated at Turku University Hospital were re-examined and divided into three histological grades of differentiation, four grades of keratinisation, and four grades of p53 and bcl-2 immunostaining. The apoptosis in-situ was assessed by TUNEL and was analysed as the number of apoptosis per volume corrected high power fields. The percentages of cells containing tumour nuclei with one to more than four AgNORs were counted. The patient median age was 65, the disease-free 5-year survival was 53% and the overall survival rate was 64%. In univariate analysis, nodal status, tumour size and general condition were associated with disease-free and overall survival. In a subgroup of patients with T1-2N0 glottic cancer receiving definitive irradiation therapy (n = 25), small tumour size and good histological differentiation were associated with good disease-free and overall survival. Apoptosis associated and proliferative markers did not seem to have more value to prediction of clinical outcome than the common clinical parameters.