This paper investigated the internal factors that affecting profitability of banks. The main objective was to compare the profitability of the Saudi and Jordanian banks by using the internal factors for estimations. The necessary data was collected from secondary sources. A sample of twenty three Saudi and Jordanian banks was considered with 161 observations for the period 2005-2011. Financial ratios were calculated and statistical tools including Pearsonís correlation, descriptive analysis of variance and regression analysis were utilized in testing the hypotheses and to measure the differences and similarities between the sample banks according to their different characteristics. The factors influencing the profitability were tested empirically. However, the results indicated that there is a significant positive correlation between ROA of Saudi banks with TEA, TIA and LQR variables, as well as a negative correlation with NCA, CDR, CIR and SZE variables. Meanwhile, there is a significant positive correlation between ROA of Jordanian banks with LQR, NCA, TEA and CDR variables, also there is a negative correlation of return on assets with CIR, TIA and SZE. It is recommended that empirical studies should be undertaken in the same field to find out what more internal factors could affect profitability of banks.