Objectives: To study the correlation between whole salivary secretion rates and different variables from the radionuclide time-activity curve and to determine a reliable region for background correction in salivary gland scintigraphy. Methods: Salivary gland scintigraphy (SGS) was performed before bone marrow transplantation or more than 4 years later in 23 patients aged 13.5 (s.d. 4.9) years. Unstimulated and stimulated whole salivary secretion rates were measured before SGS. Six different methods for background correction were evaluated. Results: The unstimulated secretion rate was significantly correlated (P<0.05) with the percentage stimulated secretion (S) and reaccumulation-slope (RS) after stimulation. The stimulated secretion rate was significantly correlated with RS, S and down-slope (DS). The temporal region above the parotid glands and the area above the thyroid gland was used for subtraction of background radiation for the parotid and submandibular glands respectively showed a strong correlation between repeated measurements of the variables analysed. The mean maximum uptake was 0.73-1.34% of total dose injected. Conclusions: The salivary scintigraphic variables which correlated more strongly with salivary secretion rates were RS, S and DS. The temporal region above the parotid gland and the area above the thyroid gland can be used reliably for correction background radiation in the analysis of the time-activity curve in SGS of the parotid and submandibular glands respectively.