Abstract Background Autologous mesenchymal stem cells (MSC) from different origins, including adipose tissue, have been proposed for the treatment of anal incontinence with encouraging preclinical and clinical outcomes. Cell transplantation as tridimensional structures instead of individual cell suspension seems to increase cell viability and implantation. We previously developed a protocol for MSC isolation directly from haemorrhoidal tissue (he-MSC) in human and demonstrated that the isolated cells fulfil MSC criteria. Aims Evaluate the characteristics and secretome of he-MSC in both two-dimensional or tridimensional cultures. Methods Informed consent was obtained from all patients. Tissue samples were procured from haemorrhoidectomy specimens or liposuction waste product and processed and characterized according to previously reported methods. He-MSC were cultured as spheroids using the “hanging-drop technique” or agarose pits. Immunofluorescence was performed to assess the expression of mesenchymal proteins and cell viability. Conditioned media of tow-dimensional cultures or spheroids in suspension were generated using low serum culture medium and analysed with semi-quantitative cytokine arrays (120 cytokines) and ELISA assays. Results Cultured cells demonstrated expression of vimentin and good viability, even as spheroids (2.6±2% cell death). Cytokine profile of he-MSC secretome was similar to that of adipose tissue-derived MSC (AT-MSC), with shared core cytokines (FGF-9, OPG, CCL2, CCL11, CCL13, IGFBP-4, IGFBP-6). Concentration of HGF measured by ELISA was higher in he-MSC conditioned medium than in AT- MSC conditioned medium (19613±3528 versus 179±84 pg/ml p<0.001) whereas VEGF concentration followed an opposite trend (7627±947pg/ml versus 181±74 pg/ml p<0.001). Production of mesenchymal proteins and growth factors was not affected by the spheroid configuration of cells. Conclusion We demonstrated that he-MSC exhibit a similar secretome profile compared to AT-MSC. Generation of spheroids did not compromise cell viability or their ability to produce structural proteins and growth factors, validating he-MSC spheroids use for further in vivo studies prior to clinical validation.