We analyse the clustering properties of a high-resolution (similar to
10 km s(-1)) sample of about 1600 Lyman alpha lines in the spectra of
15 quasars, obtained in the framework of an ESO key programme with the
addition of literature data. The two-point correlation function in ve
locity space shows a significant signal on small velocity scales (Delt
a v less than or similar to 300 km s(-1)) with amplitude and significa
nce increasing with increasing column density. The correlation scale a
t z similar to 3 turns out to be 200-300 h(50)(-1) kpc. A trend of inc
reasing correlation with decreasing redshift is apparent. The existenc
e of over- and underdensities on scales of a few tens of Mpc is confir
med with a high confidence level and a number of possible structures a
re identified. The present observation are found to be consistent with
models of gravitationally induced correlations. A continuity scenario
between Lyman alpha and metal systems emerges, with a suggested physi
cal association between the Lyman alpha clouds with log N-HI greater t
han or similar to 14 and the haloes of protogalactic systems.