In this study, the effect of different storage temperatures (25, 35 and 45°C) and storage times (0, 45 and 90 days) on physicochemical properties (color values, pH, and brix) and HMF (5-hydroxymethylfurfural) contents of grape, mulberry, black mulberry and carob molasses samples was studied. A two factor-three level composite face center design was performed to model and study effects of these factors on the HMF contents of these samples. As a result, storage temperature and time values were found to remarkably change the physicochemical properties and HMF contents. HMF content of the molasses samples increased with temperature and storage time. The highest HMF levels were generally observed in mulberry and black mulberry molasses. The best fitting second order polynomial models were developed using multiple linear regression analysis with backward elimination regression (BER) procedure to remove insignificant factors and interactions from the models. R2 values of the established models were higher than 0.844, indicating that models were adequate to predict HMF content. © 2013 Elsevier B.V.