This paper presents the first direct estimate of the 3D clustering properties of far-infrared sources up to z˜ 3. This has been possible thanks to the PACS Evolutionary Probe (PEP) survey of the GOODS-South field performed with the PACS instrument on board the Herschel satellite. 550 and 502 sources were detected respectively in the 100- and 160-μm channels down to fluxes ? mJy and ? mJy, cuts that ensure >80 per cent completeness of the two catalogues. More than 65 per cent of these sources have an (either photometric or spectroscopic) redshift determination from the MUSIC catalogue; this percentage rises to ˜95 per cent in the inner portion of GOODS-South which is covered by data at other wavelengths. An analysis of the deprojected two-point correlation function w(θ) over the whole redshift range spanned by the data reports for the (comoving) correlation length, r0˜ 6.3 and ˜6.7 Mpc, respectively at 100 and 160 μm, corresponding to dark matter halo masses M≳ 1012.4 M&sun;, in an excellent agreement with previous estimates obtained for mid-IR selected sources in the same field. Objects at z˜ 2 instead seem to be more strongly clustered, with r0˜ 19 and ˜17 Mpc in the two considered PACS channels. This dramatic increase of the correlation length between z˜ 1 and ˜2 is connected with the presence, more visible at 100 μm than in the other band, of a wide (at least 4 Mpc across in projection), M≳ 1014 M&sun;, filamentary structure which includes more than 50 per cent of the sources detected at z˜ 2. An investigation of the properties of such sources indicates the possibility of a boosted star-forming activity in those which reside within the overdense environment with respect to more isolated galaxies found in the same redshift range. If confirmed by larger data sets, this result can be explained as due to the combined effect of large reservoirs of gas available at high redshifts in deep potential wells such as those associated with large overdensities and the enhanced rate of encounters between sources favoured by their relative proximity. Lastly, we also present our results on the evolution of the relationship between luminous and dark matter in star-forming galaxies between z˜ 1 and ˜2. We find that the increase in (average) stellar mass in galaxies between z˜ 1 and ˜2 is about a factor of 10 lower than that of the dark matter haloes hosting such objects (z˜ 1/z˜ 2˜ 4 × 10-1 versus Mz˜ 1halo/Mhaloz˜ 2˜ 4 × 10-2). When compared with recent results taken from the literature, our findings agree with the evolutionary picture of downsizing whereby massive galaxies at z˜ 2 were more actively forming stars than their z˜ 1 counterparts, while at the same time they contained a lower fraction of their mass in the form of luminous matter. Herschel is an ESA space observatory with science instruments provided by the European-led Principal Investigator consortia, with an important participation from NASA.