The aim of this study is to figure out the factors affecting mudaraba deposits in Indonesia using a well known econometric’s cointegration method. It uses quarterly time series in the period of 1993 – 2003. Four variables, GDP, number of Islamic bank’s branch offices, profit sharing rate, and interest rate are thought to have influence on the volume of mudaraba deposits. The cointegration test indicates that the number of Islamic bank’s branch offices and profit sharing rate are significantly affects the volume of mudaraba deposits in Indonesia in the long run, while GDP and interest rate are not. It may be concluded that the volume of mudaraba deposits in Indonesia does not depend on income or interest rate, but depend on profit sharing rate and the number of branch offices of the Islamic commercial banks. This finding supported the view that depositors are attracted to put their money in Indonesian Islamic banks partly due to welfare maximisation reasons, not only because of their religious considerations. Moreover, in order to increase the volume of mudaraba deposits in Indonesia, it is suggested that more branch offices of Islamic commercial banks are built. Lastly, Indonesian Islamic commercial banks should also provide an optimal profit sharing rate in order to attract more depositors.