Using a sample of approximately 14,000 z>2.1 quasars observed in the first year of the Baryon Oscillation Spectroscopic Survey (BOSS), we measure the three-dimensional correlation function of absorption in the Lyman-alpha forest. The angle-averaged correlation function of transmitted flux (F = exp(-tau)) is securely detected out to comoving separations of 60 Mpc/h, the first detection of flux correlations across widely separated sightlines. A quadrupole distortion of the redshift-space correlation function by peculiar velocities, the signature of the gravitational instability origin of structure in the Lyman-alpha forest, is also detected at high significance. We obtain a good fit to the data assuming linear theory redshift-space distortion and linear bias of the transmitted flux, relative to the matter fluctuations of a standard LCDM cosmological model (inflationary cold dark matter with a cosmological constant). At 95% confidence, we find a linear bias parameter 0.16<b<0.24 and redshift-distortion parameter 0.44<beta<1.20, at central redshift z=2.25, with a well constrained combination b(1+\beta)=0.336 +/- 0.012. The errors on beta are asymmetric, with beta=0 excluded at over 5 sigma confidence level. The value of beta is somewhat low compared to theoretical predictions, and our tests on synthetic data suggest that it is depressed (relative to expectations for the Lyman-alpha forest alone) by the presence of high column density systems and metal line absorption. These results set the stage for cosmological parameter determinations from three-dimensional structure in the Lyman-alpha forest, including anticipated constraints on dark energy from baryon acoustic oscillations.