Context. S-type AGB stars (C/O ≈ 1) are thought to be transition objects from M-type (O-rich) AGB stars to carbon stars and as such are interesting objects in themselves. Of particular interest is to determine accurate circumstellar properties and molecular abundances, due to their predicted sensitivity to the photospheric C/O-ratio. Aims. Presented here are new sensitive sub-millimetre line observations of molecules towards the S-type AGB star χ Cyg, using the HIFI instrument on-board the Herschel Space Observatory. The observed lines predominantly probe warm gas relatively close to the central star. Methods. Detailed, non-LTE, radiative transfer modelling has been used in order to interpret the circumstellar molecular line observations performed using HIFI, assuming a spherically symmetric, smooth, accelerating wind. Results. Lines from common molecules such as H 2 O, CO and SiO, which are expected to be abundant in an S-type AGB star, are clearly detected (as well as some of their isotopologues) in the HIFI spectra. In addition, we detect lines from carbon-bearing molecules such as HCN and CN. The CO line modelling indicates that the mass-loss rate has not undergone any significant modulations during the past ≈1000 yr. The derived o-H 2 O fractional abundance is ≈7 × 10 −6 , i.e., lower than those obtained for a small sample of M-type AGB stars but higher than what has been derived for a few carbon stars. We further obtain a p-H 2 O fractional abundance of ≈5 × 10 −6 giving an o/p-ratio of ≈1.4. Molecular line cooling is dominated by H 2 O only in a region close to the star ( 6 × 10 14 cm). The SiO abundance is estimated to be ≈1 × 10 −5 . The 12 CO/ 13 CO ratio is 43 ± 6. The high-excitation rotational lines clearly probe the acceleration region of the stellar wind ( 2 × 10 15 cm) and put constraints on dynamical wind models. We are unable to fit consistently the combined ground-based and HIFI data for HCN and CN. Conclusions. The derived H 2 O abundance is reasonably consistent with recent chemical model predictions and so is the SiO abundance. The o/p-ratio of ≈1.4 supports a chemical formation under non-LTE conditions for the H 2 O molecules, and the presence of carbon-bearing molecules at relatively large abundances is also indicative of the importance of non-LTE chemical processes in regulating the circumstellar chemistry. The velocity field derived from the molecular line modelling is consistent with that obtained from solving for the wind dynamics through the coupled momentum equations of the dust and gas particles.