We present a timing solution for the 598.89 Hz accreting millisecond pulsar, IGR J00291+5934, using Rossi X-ray Timing Explorer data taken during the two outbursts exhibited by the source on 2008 August and September. We estimate the neutron star spi
n frequency and we refine the system orbital solution. To achieve the highest possible accuracy in the measurement of the spin frequency variation experienced by the source in-between the 2008 August outburst and the last outburst exhibited in 2004, we re-analysed the latter considering the whole data set available. We find that the source spins down during quiescence at an average rate of { u}dot_{sd}=(-4.1 +/- 1.2)E-15 Hz/s. We discuss possible scenarios that can account for the long-term neutron star spin-down in terms of either magneto-dipole emission, emission of gravitational waves, and a propeller effect. If interpreted in terms of magneto-dipole emission, the measured spin down translates into an upper limit to the neutron star magnetic field, B<=3E+08 G, while an upper limit to the average neutron star mass quadrupole moment of Q<=2E+36 g cm^2 is set if the spin down is interpreted in terms of the emission of gravitational waves.
