We present a novel technique for calculating the two-point autocorrela
tion function of the Ly alpha forest based on the relation between the
two-point correlation function and the neighbor probability distribut
ion functions. The technique appears to reduce the scatter in estimate
s of the correlation function by a factor of similar to 2 from the tra
ditional pair-counting method. We apply the technique to the Ly alpha
forest line lists determined from the spectra of seven z > 2 QSOs obse
rved at high resolution (Delta v < 25 km s(-1)). Of these, only two sp
ectra, those of Q0055-259 and Q0014+813, appear to be sufficiently fre
e of systematics to obtain meaningful estimates of the correlation fun
ction. We find positive correlations, with a maximum amplitude of 0.5-
1, on the scale of 0.5-3 h(-1) Mpc (comoving), or 100-600 km s(-1), in
the forests of both QSOs. The technique also finds strong evidence fo
r anticorrelation on the scale of 3-6 h(-1) Mpc. The strength of the p
ositive correlations is comparable to that predicted from the primordi
al power spectrum inferred from optically selected galaxy redshift sur
veys. If the anticorrelations are physical, it becomes unclear whether
the detected clustering is consistent with current models of structur
e formation with a homogeneous photoionizing UV metagalactic backgroun
d. Instead, the anticlustering may require inhomogeneity in the UV bac
kground and possibly in the process of reionization itself.