We analyze the clustering properties of a high-resolution ( \sim 10 km/s ) 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 the velocity space shows a significant signal on small velocity scales ( \Delta v \la 300 km/s ) with amplitude and significance increasing with increasing column density . The correlation scale at z \sim 3 turns out to be 200 - 300 h _ { 50 } ^ { -1 } kpc . A trend of increasing correlation with decreasing redshift is apparent . The existence of over- and under-densities on scales of a few tens of Megaparsec is confirmed with a high confidence level and a number of possible structures are identified . The present observations are found to be consistent with models of gravitationally induced correlations . A continuity scenario between Lyman- \alpha and metal systems emerges , with a suggested physical association between the Lyman- \alpha clouds with \log N _ { HI } \ga 14 and the halos of protogalactic systems .