Context. How the diffuse medium of molecular clouds condenses in dense cores and how many of these cores will evolve in protostars is still a poorly understood step of the star formation process. Much progress is being made in this field, thanks to the extensive imaging of star-forming regions carried out with the Herschel Space Observatory. Aims. The Herschel Gould Belt Survey key project mapped the bulk of nearby star-forming molecular clouds in five far-infrared bands with the aim of compiling complete census of prestellar cores and young, embedded protostars. From the complete sample of prestellar cores, we aim at defining the core mass function and studying its relationship with the stellar initial mass function. Young stellar objects (YSOs) with a residual circumstellar envelope are also detected. Methods. In this paper, we present the catalogue of the dense cores and YSOs/protostars extracted from the Herschel maps of the Lupus I, III, and IV molecular clouds. The physical properties of the detected objects were derived by fitting their spectral energy distributions. Results. A total of 532 dense cores, out of which 103 are presumably prestellar in nature, and 38 YSOs/protostars have been detected in the three clouds. Almost all the prestellar cores are associated with filaments against only about one third of the unbound cores and YSOs/protostars. Prestellar core candidates are found even in filaments that are on average thermally subcritical and over a background column density lower than that measured in other star-forming regions so far. The core mass function of the prestellar cores peaks between 0.2 and 0.3 M_⊙, and it is compatible with the log-normal shape found in other regions. Herschel data reveal several, previously undetected, protostars and new candidates of Class 0 and Class II with transitional disks. We estimate the evolutionary status of the YSOs/protostars using two independent indicators: the α index and the fitting of the spectral energy distribution from near- to far-infrared wavelengths. For 70% of the objects, the evolutionary stages derived with the two methods are in agreement. Conclusions. Lupus is confirmed to be a very low-mass star-forming region, in terms of both the prestellar condensations and the diffuse medium. Noticeably, in the Lupus clouds we have found star formation activity associated with interstellar medium at low column density, usually quiescent in other (more massive) star-forming regions.