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 spin 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.
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